Chun lab company introduction
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Transcript of Chun lab company introduction
www.chunlab.com
Copyright 2014 ChunLab, Inc.ⓒ
ChunLab Company Introduction
Contents
2BIOINFORMATICS MADE EASY CHUNLAB
| About ChunLab| Why ChunLab| ChunLab Services
About ChunLab
BIOINFORMATICS MADE EASY CHUNLAB 4
About ChunLab
• ChunLab is a next-generation sequencing (NGS) and bioinformatics service provider offering an end to end solution from sample to discovery
• Established in Dec. 2009 by Professor Jongsik Chun of Seoul National University
• Headquarters in Seoul, Korea with a satellite office in Rockville, MD
BIOINFORMATICS MADE EASY CHUNLAB 5
Our Mission
ChunLab’s mission is to simply bioinformatics to give clients control over their NGS data
To achieve this mission, we have designed optimized analysis pipelines forvarious research disciplines (metagenomics, genomics and transcriptomics)using carefully chosen, tested algorithms and biostatistical techniques.
Furthermore, we have designed a suite of point and click software tools thatenable researchers to easily perform sophisticated visualizations, secondaryanalysis and comparative analysis.
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Professional career– Full Tenured Professor, School of Biological Sciences,
Seoul National University (SNU) (2000~Present)– Senior Researcher, Korea Research Institute
of Bioscience and Biotechnology (KRIBB)– (1998~2000) – Research Associate, University of Maryland,
USA(1996~1998)
– Associate Editor, IJSEM (2002~2014)– Editorial Board , A Van Leeuw. J. Microb. (1999~present)
Microb. Environ. (2005~Present)– Founding Director, Bioinformatics Institute,
Seoul National University (2010).
About Dr. Jongsik Chun, CEO of ChunLab
Why ChunLab?
BIOINFORMATICS MADE EASY CHUNLAB 8
Why ChunLab?
Intuitive point & click user interfaces with advanced visualization and analytical tools
Standalone Windows and MAC based applicationsData results provided in sophisticated publication ready visualizationsExportation of data into Excel, text or FASTA formats for further downstream
analysesNo expertise in PERL, Python, C, C++ required
CLcommunityTM
for Microbial Community Analysis
CLgenomicsTM
for Whole Genome Analysis
CLRNASeqTM
for Transcriptomics Analysis
Suite of software tools designed for specific research disciplines
BIOINFORMATICS MADE EASY CHUNLAB 9
List of highly curated proprietary reference databases
EZTaxon
EZGenome
EZFungi
• Database of 16S rDNA sequences of species type strains for valid and invalid names• 63,000+ 16S rRNA gene sequences for Bacteria & Archaea (Nov 2014)• 9,900 users world wide• >2,600 citations
• Database of manually curated prokaryote genomes• > 25,000 prokaryote genomes as of Nov 2014
• Database of highly curated fungal strains using the ITS region• >17,000 fungi species as of Nov 2014
Why ChunLab?
For more information visit us at http://www.ezbiocloud.net
EZRNASeq • Need description to be launched?????
EZEcology • Need description to be launched?????
BIOINFORMATICS MADE EASY CHUNLAB 10
Composed of Ph.D. and master level bio scientists, bioinformatics specialists and software developers
Why ChunLab?
To provide…
• Consultation on the best platform(s) and study design for a success research project
• NGS and bioinformatics training (through workshops and webinars)
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Equipped with State-of-the-Art Facilities and NGS Platforms
Why ChunLab?
BIOINFORMATICS MADE EASY CHUNLAB 12
Why ChunLab?
Over 400 government and research agencies, medical centers, companies and universities using ChunLab’s services worldwide
BIOINFORMATICS MADE EASY CHUNLAB 13
What Our Clients Are Saying
It has been a pleasure working with ChunLab. At every step of the way, ChunLab members assisted with shipping/customs, sample preparation, and data generation. Their knowledge of microbial systems, in particular, sets this group apart from other genomic facilities. The resulting publication would not have been possible without the extra input and analysis of results by ChunLab team members.
Dr. Shana K. GoffrediAsst. Professor | Occidental College (USA)
”“
We are very happy with the genome sequencing and analysis results ChunLab provided us with and we would certainly recommend ChunLab to our colleagues. I do not have any genome-sequencing projects planned for next year, but ChunLab will definitely be my first choice when I next want a bacterial genome sequenced.
Dr. Paul MeyersProfessor | Dept of Molecular & Cell Biology, Univ of Cape Town
”“
Yes I was able to download all the software and use it to analyze my data. It is very user-friendly. Overall we are very satisfied with your service and quality of the data. ”
“Dr. Jing WangResearcher | Instit. of Molecular and Cell Biology (Singapore)
ChunLab ServicesMicrobiome / Microbial Community Analysis
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Microbiome/Microbial Community Analysis
• ChunLab provides a full service solution for microbiome / microbial community analysis using the 16S rRNA gene (bacteria and archaea) and the ITS region (fungi)
• Service includes: Library preparation, sequencing on Roche 454 or Illumina MiSeq platforms, comprehensive data analysis, and the delivery of results via our easy to use software browser, CLcommunity
• Bioinformatics only services also available
BIOINFORMATICS MADE EASY CHUNLAB 16
ChunLab’s Microbial Community Bioinformatics Pipeline*
Remove chimeric sequences
Taxonomic assignment using the EzTaxon and EzFungi databases**
Cluster reads for de-noising
Trim primers using pairwise alignment and the Hidden Markov Model
Paired end merge
Filter low quality sequences
Calculation of diversity index using various statistical analyses
Creation of CLC format files to be viewed in CLcommunity
*Above pipeline is for MiSeq generated data. Processing steps may vary for 454 generated data or change according to client requests and need**ChunLab provides superior phylogenetic identification and taxonomic assignment using our own highly curated in-house databases.
BIOINFORMATICS MADE EASY CHUNLAB 17
CLcommunityTM
CLcommunity is our most versatile and easy-to-use software package specially created for the purpose of visualizing next generation sequenced (NGS) data to identify and quantify species within a given microbial community.
Software Highlights:
• Free software that reads only CLC (ChunLab Community) formatted files that are generated
through ChunLab’s analysis pipeline
• ChunLab’s analysis pipeline can analyze NGS data generated from any platform
(454, MiSeq, Ion Torrent, etc)
• Ability to browse and compare up to 100 samples simultaneously
• Analyses available: taxonomic compositions as bar, pie or KRONA charts; microbial source
tracking; clustering heat maps; rarefaction curves; rank abundance; diversity indices; taxonomic
exclusivity analysis, Canonical Correspondence Analysis (CCA); Fast Unifrac Analysis; BLAST
searches
BIOINFORMATICS MADE EASY CHUNLAB 18
CLcommunity for Microbial Community Analysis
Main Browser Interactive taxonomic composition chart
Taxonomic composition as a pie chart with ability to view changes in time series data
Krona Chart
BIOINFORMATICS MADE EASY CHUNLAB 19
CLcommunity – View Taxonomic Similarity in Heat MapsHeat Map Rarefaction Curve
Canonical Correspondence Analysis (CCA) Diversity Indices
ChunLab Services
RNA Sequencing Analysis
BIOINFORMATICS MADE EASY CHUNLAB 21
RNA Sequencing Analysis
• ChunLab provides a full service solution for RNA Sequencing analysis (bacteria, human, mouse, etc)
• Service includes: Library preparation, sequencing on Illumina HiSeq 2500, comprehensive data analysis, and the delivery of results via our easy to use software browser, CLRNASeq
• Bioinformatics only services also available
BIOINFORMATICS MADE EASY CHUNLAB 22
CLRNASeqTM
Our suite of robust CLRNASeq solutions is developed for discovering, profiling and quantifying RNA transcripts. Each CLRNASeq software solution has an intuitive interface with point and click menu options that give users the power to browse mRNA mappings easily.
Software Highlights:• Free software that reads only CLT (ChunLab transcriptomics) and CLG (ChunLab Genome) formatted files that are
generated through ChunLab’s analysis pipeline
• ChunLab’s analysis pipeline can analyze NGS data generated from any platform
• Can browse and compare up to 20 samples simultaneously
• Analyses available: gene expressions analysis, differentially expressed genes; clustering of gene sets with similar
expression patterns; KEGG and eggNOG metabolic pathway analysis; SNP / InDel analysis; expression profiling;
normalization using RPKM , RLE and TMM algorithms
BIOINFORMATICS MADE EASY CHUNLAB 23
CLRNASeq for Transcriptomics AnalysisTranscript gene expressions mapped to
reference genome Differential Expression Gene Analysis
KEGG Metabolic Pathway Analysis Read Normalization using RPKM, TMM and RLE
BIOINFORMATICS MADE EASY CHUNLAB 24
CLRNASeq for Transcriptomics Analysis
SOM
Hierarchical
K-Means
Choose from 3 different clustering methods
ChunLab ServicesMicrobial Genome Analysis
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Microbial Genome Analysis
• ChunLab provides a full service solution for Microbial Genome Analysis (Bacteria, Fungi, Virus, etc)
• Service includes: Library preparation, sequencing on Illumina MiSeq or PacBio, data analysis (assembly, annotation and gene by gene genome comparisons); and the delivery of results via our easy to use software browser, CLgenomics
• Bacterial genomes present in our academic database (EzGenome) can also be freely visualized and analyzed in our CLgenomics software (for more information visit wwww.ezbiocloud.net)
• Bioinformatics only services also available
BIOINFORMATICS MADE EASY CHUNLAB 27
CLgenomicsTM Genome Browser
CLgenomics is a powerful desktop application
specifically designed to deliver insights into
microbial genomes at the click of button.
3 Main Functions of CLgenomics:
1) Multiple genome browser – easy gene finding, explore gene functions, view COG distributions and other
detailed statistics: coverage, GC ratio, genome size, contigs (N50), scaffold, CDS, etc.
2) Analytic tool -- comparative genome analysis and BLAST searches
3) Data transformer – instantly creates reports and graphs such as circular genome mappings (rRNA, tRNA, CDS,
GC ratio, GC skew); exports raw sequence data and statistics as Excel, Word, FASTA, GenBank formats or files
for NCBI submission
NOTE:
• CLgenomics can only view CLG (ChunLab Genomics) and CG (Comparative Genomics) format files that are generated through
ChunLab’s bioinformatics pipeline
BIOINFORMATICS MADE EASY CHUNLAB 28
CLgenomics for Microbial Genome Analysis
Genome Mapping
Genome browsers with simultaneous comparison of several genomes
Gene by gene genomic comparison
BIOINFORMATICS MADE EASY CHUNLAB 29
CLgenomics for Microbial Genome Analysis
Translation, ribosomal structure and biogenesis, 123
Transcription, 86
Replication, recombination and repair, 92
Cell cycle control, cell division, chromosome partitioning, 17
Posttranslational modification, protein turnover, chaperones, 40
Cell wall/membrane/envelope
biogenesis, 88
Cell motility, 5
Inorganic ion transport and metabolism, 48
Signal transduction mechanisms, 43
Energy production and conversion, 43
Carbohydrate transport and
metabolism, 85
Amino acid transport and metabolism, 59
Nucleotide transport and metabolism, 56
Coenzyme transport and metabolism, 28
Lipid transport and metabolism, 24
Secondary metabolites biosynthesis, transport and catabolism, 5
General function prediction only, 129
Function unknown, 127
Weissella Koreensis JC2156
COG Browser
COG Distribution
COG Distribution Comparison
BIOINFORMATICS MADE EASY CHUNLAB 30
CLgenomics -- Genome BLAST Function
Genome BLAST function
Export Data for NCBI Submission
Data plot using MUMmer
ChunLab’s Other Services
BIOINFORMATICS MADE EASY CHUNLAB 32
Physical Genome Mapping based on the Bionano Irys System
The Irys System generates high resolution genome maps of extremely long DNA (hundreds of kbs to more than a megabase long) without amplification, providing long-range contiguity of the genome.
Applications: • Reveal order and orientation of functionally relevant components of complex
genomes• Provide comprehensive SV (structural variation) detection and epigenetic
modifications that NGS misses• Provide reference genome validation, gap sizing and haplotyping• Eliminate re-sequencing bias
Genome maps are delivered via the IrysView Software, where genome map to map comparisons are possible. In addition, NGS contig data can be imported to finish complex genomes, validate NGS assemblies, and detect structural variations
BIOINFORMATICS MADE EASY CHUNLAB 33
Gene Expression Profiling Based on NanoString Technology
• The nCounter Analysis System from NanoString Technologies offers a simple, cost-effective way to profile hundreds of mRNAs, microRNAs, or DNA targets simultaneously with high sensitivity and precision. • Highly reproducible with no amplification needed
• Ability to probe 800 genes simultaneously
Ideal for:• Formalin-Fixed Paraffin-Embedded (FFPE) samples• Low input volume samples (starting from 100ng or less of total RNA)• Cell or blood lysates
Applications:• Gene expression profiling• Fusion genes• Copy Number Variation (CNV)• Single cell gene expression
BIOINFORMATICS MADE EASY CHUNLAB 34
For more information visit us at www.chunlab.com or contact us at [email protected]
Korea HQSeoul National University, Bldg 105-1, Suite #307, 1 Gwanok-ro, Gwanak-gu, Seoul, Korea 151-742, Tel: +82-2-875-2501
ChunLab USA9601 Medical Center Drive, Suite 326, Rockville, MD 20850, Tel: +1-240-731-8527