Post on 07-Oct-2020
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis
App name Sequencing application(s) Key functionality Vendor
Amplicon DSDemo Data Link
bull Targeted Resequencing (TruSight Tumor 26 Panel)
bull Alignmentbull Somatic Variant Callingbull Annotation
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 150 bp cost = 070 iCreditssample
BWA AlignerDemo Data Link
bull Whole Genome Sequencingbull Targeted Sequencing
bull Alignmentbull Custom reference genomebull Batch processing
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 M reads 2 x 150 bp cost = 2810 iCreditssample
BWA EnrichmentDemo Data Link
bull Targeted Resequencing bull Alignmentbull Small Variant Callingbull Annotationbull Custom Manifest Filesbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 30 M reads 2 x 75 bp cost = 528 iCreditssample
Cancer Variant CallerDemo Data Link
bull Whole-Genome Sequencingbull Targeted Resequencing
bull Variant Calling Samsung
basespaceqasamsungcom Compute Cost 3 iCredits per nodehr License Cost na
EDGC Annotator
bull Targeted Resequencing bull Variant Annotationbull Variant Analysis
EONE-DIAGNOMICS Genome Center
wwwedgccomedgcannotatorlang=en Compute Cost 3 iCredits per nodehr License Cost na
EnrichmentDemo Data Link
bull Targeted Resequencing bull Alignmentbull Small Variant Callingbull Somatic Variant Callingbull SVCNV Callingbull Annotationbull Custom Manifest Filesbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Exome (200x mean coverage) 60 M reads 2 x 75 bp cost = 676 iCreditssample
BaseSpacereg Sequence Hub Apps Quick GuideCredits are the common currency in which BaseSpace Sequence Hub services are priced Learn more about iCredits and billing
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis (continued)
App name Sequencing application(s) Key functionality Vendor
GeneTalk Variant Analyzer
bull Targeted Resequencing bull Variant Annotationbull Variant Analysis
GeneTalk
wwwgene-talkdeCompute Cost Free License Cost na
LoFreq Rare Variant CallerDemo Data Link
bull Targeted Resequencingbull Oncology
bull Variant Caller Genome Institute of Singapore
wwwgisappsorglofreqbscontacthtmCompute Cost 3 iCredits per nodehr License Cost - 1 iCredit per 10 GB of input file - 4 iCredits for 30ndash39 GB - 5 iCredits 40ndash49 GB - etc
Melanoma Profiler
bull Targeted Resequencingbull Oncology
bull Variant Analysisbull Tumor Normal
Biomatters Ltd
appsbiomatterscommelanoma-profilerwelcome Compute Cost Free
mtDNA Variant AnalyzerDemo Data Link
bull Targeted Resequencingbull mtDNA Profilingbull Forensics
bull Visualizatoinbull Variant Analysis
Illumina Inc
Compute Cost FreeLicense Cost na
mtDNA Variant ProcessorDemo Data Link
bull Targeted Resequencingbull mtDNA Profilingbull Forensics
bull mtDNA Variant Calling Illumina Inc
Compute Cost Free License Cost na
MutationForecaster
bull RNA-Seqbull Variant Analysis
bull Interpret and validate mutations that affect mRNA splicing and protein coding
Cytognomix Inc
basespacemutationforecastercomCompute Cost Free License Cost - 1 Day Subscription 75 iCredits - 7 Day Subscription 125 iCredits
MyFLqDemo Data Link
bull Forensics bull STR and SNP query University Ghent
forensicugentbeCompute Cost 3 iCredits per nodehrLicense Cost na
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis (continued)
App name Sequencing application(s) Key functionality Vendor
Novoalign Generic DNA pipelineDemo Data Link
bull Resequencing bull Alignmentbull Variant Calling
Novocraft
wwwnovocraftcomproductsnovoalignCompute Cost 3 iCredits per nodehr
NuGEN Ovation Target EnrichmentDemo Data Link
bull Targeted Resequencing bull Demultiplexingbull Alignment
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehrLicense Cost na
Phy-Mer
bull Mitochondrial Analysis bull Haplogroup Analysis MEEI Bioinformatics Center (MBC)
githubcomdanielnavarrogomezphy-merCompute Cost 3 iCredits per nodehrLicense Cost na
TruSeqreg AmpliconDemo Data Link
bull Targeted Resequencing bull Alignmentbull Small Variant Callingbull Somatic Variant Callingbull Annotationbull Custom Manifest Filesbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSight Myeloid Panel (5000x mean coverage) 235 M reads 2 x 150 bp cost = 078 iCreditssample
TruSeq Long-Read AssemblyDemo Data Link
bull TruSeq Synthetic Long Reads
bull Assembly of synthetic long reads
bull Phasing Analysis
Illumina Inc
Compute Cost Free License Cost na
TruSeq Phasing AnalysisDemo Data Link
bull Genetic Analysisbull Haplotype Resolution
bull Phasing Analysis Illumina Inc
Compute Cost Free License Cost na
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis (continued)
App name Sequencing application(s) Key functionality Vendor
TruSight Tumor 15Demo Data Link
bull Targeted Resequencing (TruSight Tumor 15 Panel)
bull Alignmentbull Variant Calling
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSight Tumor 15 Panel (5000x mean coverage) 733 K reads 2 x 150 bp cost = 035 iCreditssample
TruSight Tumor 170
bull Targeted Resequencing (TruSight Tumor 170 Panel)
bull Variant Callingbull SVCNV Callingbull RNA Fusion Calling
Illumina Inc
Compute Cost FreeLicense Cost na
Tumor NormalDemo Data Link
bull Whole Genome Sequencing bull Variant Callingbull SVCNV Callingbull Annotationbull Tumor Normal Analysis
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost Whole Genome (80x Tumor40x Normal mean coverage) 18 B reads 2 x 100 bp cost = 9288 iCreditspair of samples
Whole Genome SequencingDemo Data Link
bull Whole Genome Sequencing bull Alignmentbull Small Variant Callingbull SVCNV Callingbull Annotationbull Batch Processing
Illumina Inc
Compute Cost 3iCredits per nodehr License Cost naWhole Genome (30x mean coverage)300 M reads 2 x 150 bpcost = 9ndash12 iCreditssample depending on sample quality
CrossMapDemo Data Link
bull Data conversion bull Converts genome coordinates between different assemblies
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization
App name Sequencing application(s) Key functionality Vendor
Elastic Genome Browser
bull Resequencing (human) bull Genome Browserbull Visualizatoins
Strand Life Sciences
wwwstrandlscomCompute Cost Free License Cost na
FASTA Upload
bull Data Import bull Import FASTA files BioBam Bioinformatics SL
wwwbiobamcombasespaceappsCompute Cost Free License Cost na
FASTQ Toolkit
bull FASTQ Manipulation bull Sub-samplingbull Adapter Trimmingbull Base Trimmingbull Quality Trimmingbull Read Filtering
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehrLicense Cost na
FASTQCDemo Data Link
bull Data QC bull Base QC Profile BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na
Genome Profiler
bull Resequencing (human) bull Genome Browserbull Visualizations
Biomatters Ltd
appsbiomatterscommelanoma-profilerwelcomeCompute Cost FreeLicense Cost na
Integrative Genomics Viewer
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Genome Browserbull Visualizations
BaseSpace Labs
basespacelabsilluminacomCompute Cost Free License Cost na
SRA Import
bull Data Importbull General NGS
bull Imports NGS data from NCBI Sequence Read Archive to BaseSpace Sequence Hub using SRA accession number
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
SRA Submission
bull Data Exportbull General NGS
bull Submission of data to NCBI SRA
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization (continued)
App name Sequencing application(s) Key functionality Vendor
USC BigWig GeneratorDemo Data Link
bull Data Conversion bull Convert data to BigWig file format
Ramsingh Lab Keck-Hematology
githubcomRamsinghLabCompute Cost 3 iCredits per nodehr License Cost na
Variant Calling Assessment ToolDemo Data Link
bull Data QC bull Comparison of variant call sets
bull SNV and Indel statistics
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Gene Expression and Regulation
App name Sequencing application(s) Key functionality Vendor
ChIPSeqDemo Data Link
bull DNA-Protein Interactionsbull ChIPSeq
bull Uses MACS for peak identificatoin and HOMER for motif discovery
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Cufflinks Assembly amp DEDemo Data Link
bull Transcriptome Miningbull Gene Expressoin
bull Assembly of novel transcripts
bull Differential Expression
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 1125 iCreditssample total RNA 50 M reads 2 x 75 bp cost = 2349 iCreditssample
DESeq2Demo Data Link
bull Transcriptome Miningbull Gene Expression
bull Differential Expression BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 3764 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 7528 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
Genomatix Pathway System (GePS)Demo Data Link
bull Transcriptomebull ChIP-Seqbull Methyl-Seqbull Oncology
bull Pathway Analysisbull Genomatix
Genomatix
wwwgenomatixdeCompute Cost Free License Cost 7 Day Subscription 70 iCredits
iPathwayGuide
bull Transcriptomebull Proteomics
bull Pathway Analysis Advaita Bio
wwwadvaitabiocomCompute Cost Free License Cost - Single Report 149 iCredits- Annual Subscription 1995 iCredits
MethylSeqMethylKit Demo Data Link
bull Methylation Profilingbull Whole Genome Sequencingbull Targeted Sequencing
bull Analyze WGBS and targeted bisulfite sequencing data
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
MethylSeq
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Alignmentbull Methylation Callingbull Custom manifestsbull Custom Genomebull Batch Processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Methyl Capture 55 M reads 2 x 100 bp cost = 1953 iCreditssample
miRNAs AnalysisDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Differential Expression
BampGu University of Torino
mirnasanalysisbasespaceappblogspotit Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 M reads 1 x 50 bp cost = 078 iCreditssample
NextBio Annotates RNA-SeqDemo Data Link
bull Transcriptomebull Gene Expression
bull Gene Annotation using BaseSpace Correlation Engine
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
NuGEN Ovation Fusion DetectionDemo Data Link
bull Targeted RNA-Seq bull Alignmentbull Fusion Detection
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
RNA ExpressDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Assembly of novel transcripts with STAR
bull Differential Expression with DESeq
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 228 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 455 iCreditssample
RNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Alignment (STAR or TopHat)bull Gene Countsbull Transcripts Countsbull Annotationbull Variant Callingbull Fusion Detectinbull Novel Transcript Assemblybull Batch Processing
Illumina Inc
18 License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 602 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 1204 iCreditssample
Small RNASequencing
Small RNADemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SureCell RNA Single-CellDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Cell Countsbull Alignmentbull Gene Countsbull Cell Filteringbull Transcripts Countsbull Reporting
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost1000 cells 100 K readscell 100 M reads 1 x 75 bp cost = 815 iCreditssample
TruSeq Targeted RNADemo Data Link
bull Targeted Gene Expression bull Gene Expression Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics
App name Sequencing application(s) Key functionality Vendor
16s Metagenomics
16S MetagenomicsDemo Data Link
bull 16S rRNA Microbial Communities Profiling
bull Taxonomic classification of microbial communities
bull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample
DeepChekreg-HBVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits
DeepChekreg-HCVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits
DeepChekreg-HIVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits
GENIUS Metagenomics Know NowDemo Data Link
bull Metagenomics bull Bacterial ID CosmosID
wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na
IgReCDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Reconsts full-length adaptive immune repertoires from Rep-Seq data
bull Alignment
Center for Algorithmic Biotech
yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na
Kraken MetagenomicsDemo Data Link
bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis (continued)
App name Sequencing application(s) Key functionality Vendor
GeneTalk Variant Analyzer
bull Targeted Resequencing bull Variant Annotationbull Variant Analysis
GeneTalk
wwwgene-talkdeCompute Cost Free License Cost na
LoFreq Rare Variant CallerDemo Data Link
bull Targeted Resequencingbull Oncology
bull Variant Caller Genome Institute of Singapore
wwwgisappsorglofreqbscontacthtmCompute Cost 3 iCredits per nodehr License Cost - 1 iCredit per 10 GB of input file - 4 iCredits for 30ndash39 GB - 5 iCredits 40ndash49 GB - etc
Melanoma Profiler
bull Targeted Resequencingbull Oncology
bull Variant Analysisbull Tumor Normal
Biomatters Ltd
appsbiomatterscommelanoma-profilerwelcome Compute Cost Free
mtDNA Variant AnalyzerDemo Data Link
bull Targeted Resequencingbull mtDNA Profilingbull Forensics
bull Visualizatoinbull Variant Analysis
Illumina Inc
Compute Cost FreeLicense Cost na
mtDNA Variant ProcessorDemo Data Link
bull Targeted Resequencingbull mtDNA Profilingbull Forensics
bull mtDNA Variant Calling Illumina Inc
Compute Cost Free License Cost na
MutationForecaster
bull RNA-Seqbull Variant Analysis
bull Interpret and validate mutations that affect mRNA splicing and protein coding
Cytognomix Inc
basespacemutationforecastercomCompute Cost Free License Cost - 1 Day Subscription 75 iCredits - 7 Day Subscription 125 iCredits
MyFLqDemo Data Link
bull Forensics bull STR and SNP query University Ghent
forensicugentbeCompute Cost 3 iCredits per nodehrLicense Cost na
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis (continued)
App name Sequencing application(s) Key functionality Vendor
Novoalign Generic DNA pipelineDemo Data Link
bull Resequencing bull Alignmentbull Variant Calling
Novocraft
wwwnovocraftcomproductsnovoalignCompute Cost 3 iCredits per nodehr
NuGEN Ovation Target EnrichmentDemo Data Link
bull Targeted Resequencing bull Demultiplexingbull Alignment
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehrLicense Cost na
Phy-Mer
bull Mitochondrial Analysis bull Haplogroup Analysis MEEI Bioinformatics Center (MBC)
githubcomdanielnavarrogomezphy-merCompute Cost 3 iCredits per nodehrLicense Cost na
TruSeqreg AmpliconDemo Data Link
bull Targeted Resequencing bull Alignmentbull Small Variant Callingbull Somatic Variant Callingbull Annotationbull Custom Manifest Filesbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSight Myeloid Panel (5000x mean coverage) 235 M reads 2 x 150 bp cost = 078 iCreditssample
TruSeq Long-Read AssemblyDemo Data Link
bull TruSeq Synthetic Long Reads
bull Assembly of synthetic long reads
bull Phasing Analysis
Illumina Inc
Compute Cost Free License Cost na
TruSeq Phasing AnalysisDemo Data Link
bull Genetic Analysisbull Haplotype Resolution
bull Phasing Analysis Illumina Inc
Compute Cost Free License Cost na
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis (continued)
App name Sequencing application(s) Key functionality Vendor
TruSight Tumor 15Demo Data Link
bull Targeted Resequencing (TruSight Tumor 15 Panel)
bull Alignmentbull Variant Calling
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSight Tumor 15 Panel (5000x mean coverage) 733 K reads 2 x 150 bp cost = 035 iCreditssample
TruSight Tumor 170
bull Targeted Resequencing (TruSight Tumor 170 Panel)
bull Variant Callingbull SVCNV Callingbull RNA Fusion Calling
Illumina Inc
Compute Cost FreeLicense Cost na
Tumor NormalDemo Data Link
bull Whole Genome Sequencing bull Variant Callingbull SVCNV Callingbull Annotationbull Tumor Normal Analysis
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost Whole Genome (80x Tumor40x Normal mean coverage) 18 B reads 2 x 100 bp cost = 9288 iCreditspair of samples
Whole Genome SequencingDemo Data Link
bull Whole Genome Sequencing bull Alignmentbull Small Variant Callingbull SVCNV Callingbull Annotationbull Batch Processing
Illumina Inc
Compute Cost 3iCredits per nodehr License Cost naWhole Genome (30x mean coverage)300 M reads 2 x 150 bpcost = 9ndash12 iCreditssample depending on sample quality
CrossMapDemo Data Link
bull Data conversion bull Converts genome coordinates between different assemblies
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization
App name Sequencing application(s) Key functionality Vendor
Elastic Genome Browser
bull Resequencing (human) bull Genome Browserbull Visualizatoins
Strand Life Sciences
wwwstrandlscomCompute Cost Free License Cost na
FASTA Upload
bull Data Import bull Import FASTA files BioBam Bioinformatics SL
wwwbiobamcombasespaceappsCompute Cost Free License Cost na
FASTQ Toolkit
bull FASTQ Manipulation bull Sub-samplingbull Adapter Trimmingbull Base Trimmingbull Quality Trimmingbull Read Filtering
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehrLicense Cost na
FASTQCDemo Data Link
bull Data QC bull Base QC Profile BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na
Genome Profiler
bull Resequencing (human) bull Genome Browserbull Visualizations
Biomatters Ltd
appsbiomatterscommelanoma-profilerwelcomeCompute Cost FreeLicense Cost na
Integrative Genomics Viewer
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Genome Browserbull Visualizations
BaseSpace Labs
basespacelabsilluminacomCompute Cost Free License Cost na
SRA Import
bull Data Importbull General NGS
bull Imports NGS data from NCBI Sequence Read Archive to BaseSpace Sequence Hub using SRA accession number
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
SRA Submission
bull Data Exportbull General NGS
bull Submission of data to NCBI SRA
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization (continued)
App name Sequencing application(s) Key functionality Vendor
USC BigWig GeneratorDemo Data Link
bull Data Conversion bull Convert data to BigWig file format
Ramsingh Lab Keck-Hematology
githubcomRamsinghLabCompute Cost 3 iCredits per nodehr License Cost na
Variant Calling Assessment ToolDemo Data Link
bull Data QC bull Comparison of variant call sets
bull SNV and Indel statistics
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Gene Expression and Regulation
App name Sequencing application(s) Key functionality Vendor
ChIPSeqDemo Data Link
bull DNA-Protein Interactionsbull ChIPSeq
bull Uses MACS for peak identificatoin and HOMER for motif discovery
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Cufflinks Assembly amp DEDemo Data Link
bull Transcriptome Miningbull Gene Expressoin
bull Assembly of novel transcripts
bull Differential Expression
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 1125 iCreditssample total RNA 50 M reads 2 x 75 bp cost = 2349 iCreditssample
DESeq2Demo Data Link
bull Transcriptome Miningbull Gene Expression
bull Differential Expression BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 3764 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 7528 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
Genomatix Pathway System (GePS)Demo Data Link
bull Transcriptomebull ChIP-Seqbull Methyl-Seqbull Oncology
bull Pathway Analysisbull Genomatix
Genomatix
wwwgenomatixdeCompute Cost Free License Cost 7 Day Subscription 70 iCredits
iPathwayGuide
bull Transcriptomebull Proteomics
bull Pathway Analysis Advaita Bio
wwwadvaitabiocomCompute Cost Free License Cost - Single Report 149 iCredits- Annual Subscription 1995 iCredits
MethylSeqMethylKit Demo Data Link
bull Methylation Profilingbull Whole Genome Sequencingbull Targeted Sequencing
bull Analyze WGBS and targeted bisulfite sequencing data
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
MethylSeq
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Alignmentbull Methylation Callingbull Custom manifestsbull Custom Genomebull Batch Processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Methyl Capture 55 M reads 2 x 100 bp cost = 1953 iCreditssample
miRNAs AnalysisDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Differential Expression
BampGu University of Torino
mirnasanalysisbasespaceappblogspotit Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 M reads 1 x 50 bp cost = 078 iCreditssample
NextBio Annotates RNA-SeqDemo Data Link
bull Transcriptomebull Gene Expression
bull Gene Annotation using BaseSpace Correlation Engine
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
NuGEN Ovation Fusion DetectionDemo Data Link
bull Targeted RNA-Seq bull Alignmentbull Fusion Detection
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
RNA ExpressDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Assembly of novel transcripts with STAR
bull Differential Expression with DESeq
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 228 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 455 iCreditssample
RNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Alignment (STAR or TopHat)bull Gene Countsbull Transcripts Countsbull Annotationbull Variant Callingbull Fusion Detectinbull Novel Transcript Assemblybull Batch Processing
Illumina Inc
18 License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 602 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 1204 iCreditssample
Small RNASequencing
Small RNADemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SureCell RNA Single-CellDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Cell Countsbull Alignmentbull Gene Countsbull Cell Filteringbull Transcripts Countsbull Reporting
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost1000 cells 100 K readscell 100 M reads 1 x 75 bp cost = 815 iCreditssample
TruSeq Targeted RNADemo Data Link
bull Targeted Gene Expression bull Gene Expression Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics
App name Sequencing application(s) Key functionality Vendor
16s Metagenomics
16S MetagenomicsDemo Data Link
bull 16S rRNA Microbial Communities Profiling
bull Taxonomic classification of microbial communities
bull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample
DeepChekreg-HBVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits
DeepChekreg-HCVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits
DeepChekreg-HIVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits
GENIUS Metagenomics Know NowDemo Data Link
bull Metagenomics bull Bacterial ID CosmosID
wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na
IgReCDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Reconsts full-length adaptive immune repertoires from Rep-Seq data
bull Alignment
Center for Algorithmic Biotech
yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na
Kraken MetagenomicsDemo Data Link
bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis (continued)
App name Sequencing application(s) Key functionality Vendor
Novoalign Generic DNA pipelineDemo Data Link
bull Resequencing bull Alignmentbull Variant Calling
Novocraft
wwwnovocraftcomproductsnovoalignCompute Cost 3 iCredits per nodehr
NuGEN Ovation Target EnrichmentDemo Data Link
bull Targeted Resequencing bull Demultiplexingbull Alignment
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehrLicense Cost na
Phy-Mer
bull Mitochondrial Analysis bull Haplogroup Analysis MEEI Bioinformatics Center (MBC)
githubcomdanielnavarrogomezphy-merCompute Cost 3 iCredits per nodehrLicense Cost na
TruSeqreg AmpliconDemo Data Link
bull Targeted Resequencing bull Alignmentbull Small Variant Callingbull Somatic Variant Callingbull Annotationbull Custom Manifest Filesbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSight Myeloid Panel (5000x mean coverage) 235 M reads 2 x 150 bp cost = 078 iCreditssample
TruSeq Long-Read AssemblyDemo Data Link
bull TruSeq Synthetic Long Reads
bull Assembly of synthetic long reads
bull Phasing Analysis
Illumina Inc
Compute Cost Free License Cost na
TruSeq Phasing AnalysisDemo Data Link
bull Genetic Analysisbull Haplotype Resolution
bull Phasing Analysis Illumina Inc
Compute Cost Free License Cost na
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis (continued)
App name Sequencing application(s) Key functionality Vendor
TruSight Tumor 15Demo Data Link
bull Targeted Resequencing (TruSight Tumor 15 Panel)
bull Alignmentbull Variant Calling
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSight Tumor 15 Panel (5000x mean coverage) 733 K reads 2 x 150 bp cost = 035 iCreditssample
TruSight Tumor 170
bull Targeted Resequencing (TruSight Tumor 170 Panel)
bull Variant Callingbull SVCNV Callingbull RNA Fusion Calling
Illumina Inc
Compute Cost FreeLicense Cost na
Tumor NormalDemo Data Link
bull Whole Genome Sequencing bull Variant Callingbull SVCNV Callingbull Annotationbull Tumor Normal Analysis
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost Whole Genome (80x Tumor40x Normal mean coverage) 18 B reads 2 x 100 bp cost = 9288 iCreditspair of samples
Whole Genome SequencingDemo Data Link
bull Whole Genome Sequencing bull Alignmentbull Small Variant Callingbull SVCNV Callingbull Annotationbull Batch Processing
Illumina Inc
Compute Cost 3iCredits per nodehr License Cost naWhole Genome (30x mean coverage)300 M reads 2 x 150 bpcost = 9ndash12 iCreditssample depending on sample quality
CrossMapDemo Data Link
bull Data conversion bull Converts genome coordinates between different assemblies
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization
App name Sequencing application(s) Key functionality Vendor
Elastic Genome Browser
bull Resequencing (human) bull Genome Browserbull Visualizatoins
Strand Life Sciences
wwwstrandlscomCompute Cost Free License Cost na
FASTA Upload
bull Data Import bull Import FASTA files BioBam Bioinformatics SL
wwwbiobamcombasespaceappsCompute Cost Free License Cost na
FASTQ Toolkit
bull FASTQ Manipulation bull Sub-samplingbull Adapter Trimmingbull Base Trimmingbull Quality Trimmingbull Read Filtering
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehrLicense Cost na
FASTQCDemo Data Link
bull Data QC bull Base QC Profile BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na
Genome Profiler
bull Resequencing (human) bull Genome Browserbull Visualizations
Biomatters Ltd
appsbiomatterscommelanoma-profilerwelcomeCompute Cost FreeLicense Cost na
Integrative Genomics Viewer
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Genome Browserbull Visualizations
BaseSpace Labs
basespacelabsilluminacomCompute Cost Free License Cost na
SRA Import
bull Data Importbull General NGS
bull Imports NGS data from NCBI Sequence Read Archive to BaseSpace Sequence Hub using SRA accession number
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
SRA Submission
bull Data Exportbull General NGS
bull Submission of data to NCBI SRA
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization (continued)
App name Sequencing application(s) Key functionality Vendor
USC BigWig GeneratorDemo Data Link
bull Data Conversion bull Convert data to BigWig file format
Ramsingh Lab Keck-Hematology
githubcomRamsinghLabCompute Cost 3 iCredits per nodehr License Cost na
Variant Calling Assessment ToolDemo Data Link
bull Data QC bull Comparison of variant call sets
bull SNV and Indel statistics
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Gene Expression and Regulation
App name Sequencing application(s) Key functionality Vendor
ChIPSeqDemo Data Link
bull DNA-Protein Interactionsbull ChIPSeq
bull Uses MACS for peak identificatoin and HOMER for motif discovery
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Cufflinks Assembly amp DEDemo Data Link
bull Transcriptome Miningbull Gene Expressoin
bull Assembly of novel transcripts
bull Differential Expression
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 1125 iCreditssample total RNA 50 M reads 2 x 75 bp cost = 2349 iCreditssample
DESeq2Demo Data Link
bull Transcriptome Miningbull Gene Expression
bull Differential Expression BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 3764 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 7528 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
Genomatix Pathway System (GePS)Demo Data Link
bull Transcriptomebull ChIP-Seqbull Methyl-Seqbull Oncology
bull Pathway Analysisbull Genomatix
Genomatix
wwwgenomatixdeCompute Cost Free License Cost 7 Day Subscription 70 iCredits
iPathwayGuide
bull Transcriptomebull Proteomics
bull Pathway Analysis Advaita Bio
wwwadvaitabiocomCompute Cost Free License Cost - Single Report 149 iCredits- Annual Subscription 1995 iCredits
MethylSeqMethylKit Demo Data Link
bull Methylation Profilingbull Whole Genome Sequencingbull Targeted Sequencing
bull Analyze WGBS and targeted bisulfite sequencing data
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
MethylSeq
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Alignmentbull Methylation Callingbull Custom manifestsbull Custom Genomebull Batch Processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Methyl Capture 55 M reads 2 x 100 bp cost = 1953 iCreditssample
miRNAs AnalysisDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Differential Expression
BampGu University of Torino
mirnasanalysisbasespaceappblogspotit Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 M reads 1 x 50 bp cost = 078 iCreditssample
NextBio Annotates RNA-SeqDemo Data Link
bull Transcriptomebull Gene Expression
bull Gene Annotation using BaseSpace Correlation Engine
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
NuGEN Ovation Fusion DetectionDemo Data Link
bull Targeted RNA-Seq bull Alignmentbull Fusion Detection
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
RNA ExpressDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Assembly of novel transcripts with STAR
bull Differential Expression with DESeq
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 228 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 455 iCreditssample
RNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Alignment (STAR or TopHat)bull Gene Countsbull Transcripts Countsbull Annotationbull Variant Callingbull Fusion Detectinbull Novel Transcript Assemblybull Batch Processing
Illumina Inc
18 License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 602 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 1204 iCreditssample
Small RNASequencing
Small RNADemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SureCell RNA Single-CellDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Cell Countsbull Alignmentbull Gene Countsbull Cell Filteringbull Transcripts Countsbull Reporting
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost1000 cells 100 K readscell 100 M reads 1 x 75 bp cost = 815 iCreditssample
TruSeq Targeted RNADemo Data Link
bull Targeted Gene Expression bull Gene Expression Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics
App name Sequencing application(s) Key functionality Vendor
16s Metagenomics
16S MetagenomicsDemo Data Link
bull 16S rRNA Microbial Communities Profiling
bull Taxonomic classification of microbial communities
bull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample
DeepChekreg-HBVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits
DeepChekreg-HCVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits
DeepChekreg-HIVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits
GENIUS Metagenomics Know NowDemo Data Link
bull Metagenomics bull Bacterial ID CosmosID
wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na
IgReCDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Reconsts full-length adaptive immune repertoires from Rep-Seq data
bull Alignment
Center for Algorithmic Biotech
yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na
Kraken MetagenomicsDemo Data Link
bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Biomedical and Basic Research ndash Genetic Analysis (continued)
App name Sequencing application(s) Key functionality Vendor
TruSight Tumor 15Demo Data Link
bull Targeted Resequencing (TruSight Tumor 15 Panel)
bull Alignmentbull Variant Calling
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSight Tumor 15 Panel (5000x mean coverage) 733 K reads 2 x 150 bp cost = 035 iCreditssample
TruSight Tumor 170
bull Targeted Resequencing (TruSight Tumor 170 Panel)
bull Variant Callingbull SVCNV Callingbull RNA Fusion Calling
Illumina Inc
Compute Cost FreeLicense Cost na
Tumor NormalDemo Data Link
bull Whole Genome Sequencing bull Variant Callingbull SVCNV Callingbull Annotationbull Tumor Normal Analysis
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost Whole Genome (80x Tumor40x Normal mean coverage) 18 B reads 2 x 100 bp cost = 9288 iCreditspair of samples
Whole Genome SequencingDemo Data Link
bull Whole Genome Sequencing bull Alignmentbull Small Variant Callingbull SVCNV Callingbull Annotationbull Batch Processing
Illumina Inc
Compute Cost 3iCredits per nodehr License Cost naWhole Genome (30x mean coverage)300 M reads 2 x 150 bpcost = 9ndash12 iCreditssample depending on sample quality
CrossMapDemo Data Link
bull Data conversion bull Converts genome coordinates between different assemblies
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization
App name Sequencing application(s) Key functionality Vendor
Elastic Genome Browser
bull Resequencing (human) bull Genome Browserbull Visualizatoins
Strand Life Sciences
wwwstrandlscomCompute Cost Free License Cost na
FASTA Upload
bull Data Import bull Import FASTA files BioBam Bioinformatics SL
wwwbiobamcombasespaceappsCompute Cost Free License Cost na
FASTQ Toolkit
bull FASTQ Manipulation bull Sub-samplingbull Adapter Trimmingbull Base Trimmingbull Quality Trimmingbull Read Filtering
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehrLicense Cost na
FASTQCDemo Data Link
bull Data QC bull Base QC Profile BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na
Genome Profiler
bull Resequencing (human) bull Genome Browserbull Visualizations
Biomatters Ltd
appsbiomatterscommelanoma-profilerwelcomeCompute Cost FreeLicense Cost na
Integrative Genomics Viewer
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Genome Browserbull Visualizations
BaseSpace Labs
basespacelabsilluminacomCompute Cost Free License Cost na
SRA Import
bull Data Importbull General NGS
bull Imports NGS data from NCBI Sequence Read Archive to BaseSpace Sequence Hub using SRA accession number
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
SRA Submission
bull Data Exportbull General NGS
bull Submission of data to NCBI SRA
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization (continued)
App name Sequencing application(s) Key functionality Vendor
USC BigWig GeneratorDemo Data Link
bull Data Conversion bull Convert data to BigWig file format
Ramsingh Lab Keck-Hematology
githubcomRamsinghLabCompute Cost 3 iCredits per nodehr License Cost na
Variant Calling Assessment ToolDemo Data Link
bull Data QC bull Comparison of variant call sets
bull SNV and Indel statistics
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Gene Expression and Regulation
App name Sequencing application(s) Key functionality Vendor
ChIPSeqDemo Data Link
bull DNA-Protein Interactionsbull ChIPSeq
bull Uses MACS for peak identificatoin and HOMER for motif discovery
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Cufflinks Assembly amp DEDemo Data Link
bull Transcriptome Miningbull Gene Expressoin
bull Assembly of novel transcripts
bull Differential Expression
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 1125 iCreditssample total RNA 50 M reads 2 x 75 bp cost = 2349 iCreditssample
DESeq2Demo Data Link
bull Transcriptome Miningbull Gene Expression
bull Differential Expression BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 3764 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 7528 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
Genomatix Pathway System (GePS)Demo Data Link
bull Transcriptomebull ChIP-Seqbull Methyl-Seqbull Oncology
bull Pathway Analysisbull Genomatix
Genomatix
wwwgenomatixdeCompute Cost Free License Cost 7 Day Subscription 70 iCredits
iPathwayGuide
bull Transcriptomebull Proteomics
bull Pathway Analysis Advaita Bio
wwwadvaitabiocomCompute Cost Free License Cost - Single Report 149 iCredits- Annual Subscription 1995 iCredits
MethylSeqMethylKit Demo Data Link
bull Methylation Profilingbull Whole Genome Sequencingbull Targeted Sequencing
bull Analyze WGBS and targeted bisulfite sequencing data
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
MethylSeq
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Alignmentbull Methylation Callingbull Custom manifestsbull Custom Genomebull Batch Processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Methyl Capture 55 M reads 2 x 100 bp cost = 1953 iCreditssample
miRNAs AnalysisDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Differential Expression
BampGu University of Torino
mirnasanalysisbasespaceappblogspotit Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 M reads 1 x 50 bp cost = 078 iCreditssample
NextBio Annotates RNA-SeqDemo Data Link
bull Transcriptomebull Gene Expression
bull Gene Annotation using BaseSpace Correlation Engine
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
NuGEN Ovation Fusion DetectionDemo Data Link
bull Targeted RNA-Seq bull Alignmentbull Fusion Detection
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
RNA ExpressDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Assembly of novel transcripts with STAR
bull Differential Expression with DESeq
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 228 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 455 iCreditssample
RNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Alignment (STAR or TopHat)bull Gene Countsbull Transcripts Countsbull Annotationbull Variant Callingbull Fusion Detectinbull Novel Transcript Assemblybull Batch Processing
Illumina Inc
18 License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 602 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 1204 iCreditssample
Small RNASequencing
Small RNADemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SureCell RNA Single-CellDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Cell Countsbull Alignmentbull Gene Countsbull Cell Filteringbull Transcripts Countsbull Reporting
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost1000 cells 100 K readscell 100 M reads 1 x 75 bp cost = 815 iCreditssample
TruSeq Targeted RNADemo Data Link
bull Targeted Gene Expression bull Gene Expression Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics
App name Sequencing application(s) Key functionality Vendor
16s Metagenomics
16S MetagenomicsDemo Data Link
bull 16S rRNA Microbial Communities Profiling
bull Taxonomic classification of microbial communities
bull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample
DeepChekreg-HBVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits
DeepChekreg-HCVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits
DeepChekreg-HIVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits
GENIUS Metagenomics Know NowDemo Data Link
bull Metagenomics bull Bacterial ID CosmosID
wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na
IgReCDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Reconsts full-length adaptive immune repertoires from Rep-Seq data
bull Alignment
Center for Algorithmic Biotech
yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na
Kraken MetagenomicsDemo Data Link
bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization
App name Sequencing application(s) Key functionality Vendor
Elastic Genome Browser
bull Resequencing (human) bull Genome Browserbull Visualizatoins
Strand Life Sciences
wwwstrandlscomCompute Cost Free License Cost na
FASTA Upload
bull Data Import bull Import FASTA files BioBam Bioinformatics SL
wwwbiobamcombasespaceappsCompute Cost Free License Cost na
FASTQ Toolkit
bull FASTQ Manipulation bull Sub-samplingbull Adapter Trimmingbull Base Trimmingbull Quality Trimmingbull Read Filtering
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehrLicense Cost na
FASTQCDemo Data Link
bull Data QC bull Base QC Profile BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na
Genome Profiler
bull Resequencing (human) bull Genome Browserbull Visualizations
Biomatters Ltd
appsbiomatterscommelanoma-profilerwelcomeCompute Cost FreeLicense Cost na
Integrative Genomics Viewer
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Genome Browserbull Visualizations
BaseSpace Labs
basespacelabsilluminacomCompute Cost Free License Cost na
SRA Import
bull Data Importbull General NGS
bull Imports NGS data from NCBI Sequence Read Archive to BaseSpace Sequence Hub using SRA accession number
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
SRA Submission
bull Data Exportbull General NGS
bull Submission of data to NCBI SRA
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization (continued)
App name Sequencing application(s) Key functionality Vendor
USC BigWig GeneratorDemo Data Link
bull Data Conversion bull Convert data to BigWig file format
Ramsingh Lab Keck-Hematology
githubcomRamsinghLabCompute Cost 3 iCredits per nodehr License Cost na
Variant Calling Assessment ToolDemo Data Link
bull Data QC bull Comparison of variant call sets
bull SNV and Indel statistics
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Gene Expression and Regulation
App name Sequencing application(s) Key functionality Vendor
ChIPSeqDemo Data Link
bull DNA-Protein Interactionsbull ChIPSeq
bull Uses MACS for peak identificatoin and HOMER for motif discovery
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Cufflinks Assembly amp DEDemo Data Link
bull Transcriptome Miningbull Gene Expressoin
bull Assembly of novel transcripts
bull Differential Expression
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 1125 iCreditssample total RNA 50 M reads 2 x 75 bp cost = 2349 iCreditssample
DESeq2Demo Data Link
bull Transcriptome Miningbull Gene Expression
bull Differential Expression BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 3764 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 7528 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
Genomatix Pathway System (GePS)Demo Data Link
bull Transcriptomebull ChIP-Seqbull Methyl-Seqbull Oncology
bull Pathway Analysisbull Genomatix
Genomatix
wwwgenomatixdeCompute Cost Free License Cost 7 Day Subscription 70 iCredits
iPathwayGuide
bull Transcriptomebull Proteomics
bull Pathway Analysis Advaita Bio
wwwadvaitabiocomCompute Cost Free License Cost - Single Report 149 iCredits- Annual Subscription 1995 iCredits
MethylSeqMethylKit Demo Data Link
bull Methylation Profilingbull Whole Genome Sequencingbull Targeted Sequencing
bull Analyze WGBS and targeted bisulfite sequencing data
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
MethylSeq
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Alignmentbull Methylation Callingbull Custom manifestsbull Custom Genomebull Batch Processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Methyl Capture 55 M reads 2 x 100 bp cost = 1953 iCreditssample
miRNAs AnalysisDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Differential Expression
BampGu University of Torino
mirnasanalysisbasespaceappblogspotit Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 M reads 1 x 50 bp cost = 078 iCreditssample
NextBio Annotates RNA-SeqDemo Data Link
bull Transcriptomebull Gene Expression
bull Gene Annotation using BaseSpace Correlation Engine
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
NuGEN Ovation Fusion DetectionDemo Data Link
bull Targeted RNA-Seq bull Alignmentbull Fusion Detection
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
RNA ExpressDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Assembly of novel transcripts with STAR
bull Differential Expression with DESeq
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 228 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 455 iCreditssample
RNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Alignment (STAR or TopHat)bull Gene Countsbull Transcripts Countsbull Annotationbull Variant Callingbull Fusion Detectinbull Novel Transcript Assemblybull Batch Processing
Illumina Inc
18 License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 602 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 1204 iCreditssample
Small RNASequencing
Small RNADemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SureCell RNA Single-CellDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Cell Countsbull Alignmentbull Gene Countsbull Cell Filteringbull Transcripts Countsbull Reporting
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost1000 cells 100 K readscell 100 M reads 1 x 75 bp cost = 815 iCreditssample
TruSeq Targeted RNADemo Data Link
bull Targeted Gene Expression bull Gene Expression Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics
App name Sequencing application(s) Key functionality Vendor
16s Metagenomics
16S MetagenomicsDemo Data Link
bull 16S rRNA Microbial Communities Profiling
bull Taxonomic classification of microbial communities
bull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample
DeepChekreg-HBVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits
DeepChekreg-HCVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits
DeepChekreg-HIVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits
GENIUS Metagenomics Know NowDemo Data Link
bull Metagenomics bull Bacterial ID CosmosID
wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na
IgReCDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Reconsts full-length adaptive immune repertoires from Rep-Seq data
bull Alignment
Center for Algorithmic Biotech
yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na
Kraken MetagenomicsDemo Data Link
bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Data Handling Data Quality Control (QC) and Data Visualization (continued)
App name Sequencing application(s) Key functionality Vendor
USC BigWig GeneratorDemo Data Link
bull Data Conversion bull Convert data to BigWig file format
Ramsingh Lab Keck-Hematology
githubcomRamsinghLabCompute Cost 3 iCredits per nodehr License Cost na
Variant Calling Assessment ToolDemo Data Link
bull Data QC bull Comparison of variant call sets
bull SNV and Indel statistics
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Gene Expression and Regulation
App name Sequencing application(s) Key functionality Vendor
ChIPSeqDemo Data Link
bull DNA-Protein Interactionsbull ChIPSeq
bull Uses MACS for peak identificatoin and HOMER for motif discovery
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Cufflinks Assembly amp DEDemo Data Link
bull Transcriptome Miningbull Gene Expressoin
bull Assembly of novel transcripts
bull Differential Expression
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 1125 iCreditssample total RNA 50 M reads 2 x 75 bp cost = 2349 iCreditssample
DESeq2Demo Data Link
bull Transcriptome Miningbull Gene Expression
bull Differential Expression BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 3764 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 7528 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
Genomatix Pathway System (GePS)Demo Data Link
bull Transcriptomebull ChIP-Seqbull Methyl-Seqbull Oncology
bull Pathway Analysisbull Genomatix
Genomatix
wwwgenomatixdeCompute Cost Free License Cost 7 Day Subscription 70 iCredits
iPathwayGuide
bull Transcriptomebull Proteomics
bull Pathway Analysis Advaita Bio
wwwadvaitabiocomCompute Cost Free License Cost - Single Report 149 iCredits- Annual Subscription 1995 iCredits
MethylSeqMethylKit Demo Data Link
bull Methylation Profilingbull Whole Genome Sequencingbull Targeted Sequencing
bull Analyze WGBS and targeted bisulfite sequencing data
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
MethylSeq
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Alignmentbull Methylation Callingbull Custom manifestsbull Custom Genomebull Batch Processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Methyl Capture 55 M reads 2 x 100 bp cost = 1953 iCreditssample
miRNAs AnalysisDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Differential Expression
BampGu University of Torino
mirnasanalysisbasespaceappblogspotit Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 M reads 1 x 50 bp cost = 078 iCreditssample
NextBio Annotates RNA-SeqDemo Data Link
bull Transcriptomebull Gene Expression
bull Gene Annotation using BaseSpace Correlation Engine
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
NuGEN Ovation Fusion DetectionDemo Data Link
bull Targeted RNA-Seq bull Alignmentbull Fusion Detection
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
RNA ExpressDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Assembly of novel transcripts with STAR
bull Differential Expression with DESeq
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 228 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 455 iCreditssample
RNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Alignment (STAR or TopHat)bull Gene Countsbull Transcripts Countsbull Annotationbull Variant Callingbull Fusion Detectinbull Novel Transcript Assemblybull Batch Processing
Illumina Inc
18 License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 602 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 1204 iCreditssample
Small RNASequencing
Small RNADemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SureCell RNA Single-CellDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Cell Countsbull Alignmentbull Gene Countsbull Cell Filteringbull Transcripts Countsbull Reporting
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost1000 cells 100 K readscell 100 M reads 1 x 75 bp cost = 815 iCreditssample
TruSeq Targeted RNADemo Data Link
bull Targeted Gene Expression bull Gene Expression Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics
App name Sequencing application(s) Key functionality Vendor
16s Metagenomics
16S MetagenomicsDemo Data Link
bull 16S rRNA Microbial Communities Profiling
bull Taxonomic classification of microbial communities
bull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample
DeepChekreg-HBVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits
DeepChekreg-HCVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits
DeepChekreg-HIVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits
GENIUS Metagenomics Know NowDemo Data Link
bull Metagenomics bull Bacterial ID CosmosID
wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na
IgReCDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Reconsts full-length adaptive immune repertoires from Rep-Seq data
bull Alignment
Center for Algorithmic Biotech
yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na
Kraken MetagenomicsDemo Data Link
bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
Genomatix Pathway System (GePS)Demo Data Link
bull Transcriptomebull ChIP-Seqbull Methyl-Seqbull Oncology
bull Pathway Analysisbull Genomatix
Genomatix
wwwgenomatixdeCompute Cost Free License Cost 7 Day Subscription 70 iCredits
iPathwayGuide
bull Transcriptomebull Proteomics
bull Pathway Analysis Advaita Bio
wwwadvaitabiocomCompute Cost Free License Cost - Single Report 149 iCredits- Annual Subscription 1995 iCredits
MethylSeqMethylKit Demo Data Link
bull Methylation Profilingbull Whole Genome Sequencingbull Targeted Sequencing
bull Analyze WGBS and targeted bisulfite sequencing data
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
MethylSeq
bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq
bull Alignmentbull Methylation Callingbull Custom manifestsbull Custom Genomebull Batch Processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Methyl Capture 55 M reads 2 x 100 bp cost = 1953 iCreditssample
miRNAs AnalysisDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Differential Expression
BampGu University of Torino
mirnasanalysisbasespaceappblogspotit Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 M reads 1 x 50 bp cost = 078 iCreditssample
NextBio Annotates RNA-SeqDemo Data Link
bull Transcriptomebull Gene Expression
bull Gene Annotation using BaseSpace Correlation Engine
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
NuGEN Ovation Fusion DetectionDemo Data Link
bull Targeted RNA-Seq bull Alignmentbull Fusion Detection
NuGEN Technologies Inc
wwwnugencomCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
RNA ExpressDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Assembly of novel transcripts with STAR
bull Differential Expression with DESeq
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 228 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 455 iCreditssample
RNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Alignment (STAR or TopHat)bull Gene Countsbull Transcripts Countsbull Annotationbull Variant Callingbull Fusion Detectinbull Novel Transcript Assemblybull Batch Processing
Illumina Inc
18 License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 602 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 1204 iCreditssample
Small RNASequencing
Small RNADemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SureCell RNA Single-CellDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Cell Countsbull Alignmentbull Gene Countsbull Cell Filteringbull Transcripts Countsbull Reporting
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost1000 cells 100 K readscell 100 M reads 1 x 75 bp cost = 815 iCreditssample
TruSeq Targeted RNADemo Data Link
bull Targeted Gene Expression bull Gene Expression Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics
App name Sequencing application(s) Key functionality Vendor
16s Metagenomics
16S MetagenomicsDemo Data Link
bull 16S rRNA Microbial Communities Profiling
bull Taxonomic classification of microbial communities
bull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample
DeepChekreg-HBVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits
DeepChekreg-HCVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits
DeepChekreg-HIVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits
GENIUS Metagenomics Know NowDemo Data Link
bull Metagenomics bull Bacterial ID CosmosID
wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na
IgReCDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Reconsts full-length adaptive immune repertoires from Rep-Seq data
bull Alignment
Center for Algorithmic Biotech
yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na
Kraken MetagenomicsDemo Data Link
bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Gene Expression and Regulation (continued)
App name Sequencing application(s) Key functionality Vendor
RNA ExpressDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Assembly of novel transcripts with STAR
bull Differential Expression with DESeq
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 228 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 455 iCreditssample
RNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Alignment (STAR or TopHat)bull Gene Countsbull Transcripts Countsbull Annotationbull Variant Callingbull Fusion Detectinbull Novel Transcript Assemblybull Batch Processing
Illumina Inc
18 License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 602 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 1204 iCreditssample
Small RNASequencing
Small RNADemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SureCell RNA Single-CellDemo Data LinkDemo Data Link
bull Transcriptome Miningbull Gene Expression
bull Cell Countsbull Alignmentbull Gene Countsbull Cell Filteringbull Transcripts Countsbull Reporting
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost1000 cells 100 K readscell 100 M reads 1 x 75 bp cost = 815 iCreditssample
TruSeq Targeted RNADemo Data Link
bull Targeted Gene Expression bull Gene Expression Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics
App name Sequencing application(s) Key functionality Vendor
16s Metagenomics
16S MetagenomicsDemo Data Link
bull 16S rRNA Microbial Communities Profiling
bull Taxonomic classification of microbial communities
bull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample
DeepChekreg-HBVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits
DeepChekreg-HCVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits
DeepChekreg-HIVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits
GENIUS Metagenomics Know NowDemo Data Link
bull Metagenomics bull Bacterial ID CosmosID
wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na
IgReCDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Reconsts full-length adaptive immune repertoires from Rep-Seq data
bull Alignment
Center for Algorithmic Biotech
yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na
Kraken MetagenomicsDemo Data Link
bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics
App name Sequencing application(s) Key functionality Vendor
16s Metagenomics
16S MetagenomicsDemo Data Link
bull 16S rRNA Microbial Communities Profiling
bull Taxonomic classification of microbial communities
bull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample
DeepChekreg-HBVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits
DeepChekreg-HCVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits
DeepChekreg-HIVDemo Data Link
bull Viral Typing - HBV - HCV - HIV
bull Viral Typingbull Drug Resistance
ABL SA
ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits
GENIUS Metagenomics Know NowDemo Data Link
bull Metagenomics bull Bacterial ID CosmosID
wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na
IgReCDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Reconsts full-length adaptive immune repertoires from Rep-Seq data
bull Alignment
Center for Algorithmic Biotech
yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na
Kraken MetagenomicsDemo Data Link
bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
MetaPhlAnDemo Data Link
bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab
huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na
MiXCR Immune Repertoire AnalyzerDemo Data Link
bull Targeted Sequencingbull RNA-Seqbull Immunology
bull Alignmentbull Visualization
MILaboratory
milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na
PEDANTTM SequenceAnalyzerDemo Data Link
bull Microbial bull Bacterial Sequence Analysis
Biomax Informatics AG
httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits
Prokka Genome AnnotationDemo Data Link
bull Microbial bull Prokaryotic Genome Annotation
BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
QIIME PreprocessingDemo Data Link
bull Microbiome Analysis bull Taxonomic classification of microbial communities
bull Phylogenetic reconstructionbull Batch processing
QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample
QIIME VisualizationsDemo Data Link
bull Microbiome Analysis bull Visualization QIIME Development Team
qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Microbial Genomics and Metagenomics (continued)
App name Sequencing application(s) Key functionality Vendor
Rescaf
bull Microbial bull Improves quality of scaffold sequences
BaseSpace Labs
basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na
SEAR Antibiotic ResistanceDemo Data Link
bull Metagenomicsbull Microbiome
bull Construct Antimicrobial Resistance Genes
University of Cambridge
githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na
SPAdes Genome AssemblerDemo Data Link
bull Microbial bull De novo Assembly Algorithmic Biology Lab
cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample
SRST2Demo Data Link
Demo Data Link
bull Microbial ID bull MLST Typing BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
String Graph AssemblerDemo Data Link
bull Mid-size Genome Assembler
bull Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na
Velvet de novo AssemblyDemo Data Link
bull Microbial bull de novo Assembly BaseSpace Labs
basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
Proteomics
App name Sequencing application(s) Key functionality Vendor
OpenSWATHDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
OpenSWATH Assay GeneratorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis Aebersold Group ETH Zurich
wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression AssemblerDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
Protein Expression ExtractorDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na
Protein Expression WorkflowDemo Data Link
bull Mass Specbull Proteomics
bull Protein Analysis SCIEX
sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na
RNA-Seq Translator
bull Proteomicsbull RNA-Seq
bull Uses de novo transcriptome assembly to generate protein sequences
Yale University
robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na
For Research Use Only Not for use in diagnostic procedures
copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003
wwwilluminacom
Proteomics (continued)
App name Sequencing application(s) Key functionality Vendor
Small RNASequencing
SWATH to MRM BuilderDemo Data Link
bull Small RNA sequencingbull miRNA Profiling
bull Alignmentbull Classification of miRNAs
isomiRs and piRNAsbull Novel miRNA amp pre-miRNA
discoverybull Differential Expressionbull Batch processing
Illumina Inc
Compute Cost 3 iCredits per nodehr License Cost na
SWATHAtlas Ion Library Generator
bull Proteomics bull Protein Analysis Institute for Systems Biology
wwwswathatlasorgCompute Cost Free License Cost na
Quality
App name Sequencing application(s) Key functionality Vendor
PicardSpaceDemo Data Link
bull Data QC bull Calculates alignment metrics
BaseSpace Labs
basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na