Umcp cs talk_11_3_16_v1
Transcript of Umcp cs talk_11_3_16_v1
Ben Busby, Ph.D.Genomics Outreach Coordinator
Making the Transition from Sharing Data to Sharing
KnowledgeGenomic Variation in the Rising Era of Individual Genome Sequence
but first...Better PubMed Searches!
For more information go to:ncbi.nlm.nih.gov/learn
Review of terminology and conceptsNext Generation Sequencing
Graphic Credit: Spencer Martin, UBC
Review of terminology and conceptsHow Genomes are Mapped and Assembled
© Martine Zilversmit 2013
http://1.usa.gov/1J1xmYs
NCBI NGS Online Workshop – Available on the NCBI YouTube Channel!
Review of terminology and conceptsHow Genomes are Mapped and Assembled
BioProject
BioProject
dbGaP
dbGaP
2007 2008 2009 2010 2011 2012 2013 2014 2015
14,20153,216
139,311
374,464
485,727
566,181
660,665
876,849
1,002,935
Subjects
dbGaP – GWAS and PheGenI
dbGaP – GWAS and PheGenI
dbGaP – ClinVar
ClinVar
ClinVar
ClinVar – Why Should we Care?
ClinVar – Why Should we Care?
ClinVar – Why Should we Care?
ClinVar – Why Should we Care?
ClinVar – Why Should we Care?
ClinVar – Why Should we Care?
SRA Data Structures
Investigation of NGS:SRA BLAST!
sra-search
sra-search
sra-search
Investigation of NGS:SRA BLAST!
Investigation of NGS:MagicBLAST!
Why SRA Data Structures?
sam-dump.2.6.3 --aligned-region 17:41243452-41277500 SRR925743 > BRCA1.sam
GATK (use screen or &)
.vcf from GATK
hisat2
Read Count generator (spark_genes)
GitHub Repositories
Visualizing Data on Assemblies
Visualizing SRA in the Context of RefSeq
http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000009.11&app_context=Variation_Viewer_1-1&srz=SRR1556217&v=21967751:21994490
https://goo.gl/8GPv8S
Helping Investigators make reads into [good] genomes!
The NCBI Eukaryotic Annotation Pipeline
The NCBI Prokaryotic Annotation Pipeline
Transcriptome Shotgun Assembly Database
Type Strain Databases
Targeted Locus Studies!
Making OTUs from Metagenomic DataMOLE-BLAST!
“Superbankit!”
Superbankit!
Viral Genomes
Virus Variation
Virus Variation
Virus Variation
Subscribe!
Food Borne Pathogens
Food Borne Pathogens
Food Borne Pathogens
Where to Get More Information!
Where to Get More Information!
E-Utilities (Eutils)
Video available at:http://www.ncbi.nlm.nih.gov/education/webinars/
61
E-Utilities (Eutils)
62
Introducing… Entrez DirectThe E-utilities on the UNIX
command line
esearch –db gene –query “foxp2[gene] AND human[orgn]” | \
elink –target protein –name gene_protein_refseq | \
efetch –format fasta
ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/
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Edirect Cookbook
64
Moving from FTP-scraping cron jobs to on-demand APIs
65
Edirect Cookbook (DRAFT)
66
New APIs!
67
Generating apps that work with our APIs and Data Structures,
and Improve Metadata:
NCBI Hackathons!
January 2015 4 functional software products 3 days
Hackathons
August 2015 6 Functional Software Products 3 Days
August 2015 6 Functional Software Products 3 Days
August 2015 6 Functional Software Products 3 Days
Hackathons
www.iMetric.io
An Educational Resource for RNAseq
Available to
anyone on AWS
Part of an Online Workshop
First 5 lectures
now available
on
Community Tools
www.iMetric.io
Community Tools
Community Tools
January 2016 6 Functional Software Products 3 Days
January 2016 6 Functional Software Products 3 Days
January 2016 6 Functional Software Products 3 Days
Hackathons
www.iMetric.io
January 2016
6 Functional Software Products 3 Days
Hackathons
January 2016 6 Functional Software Products 3 Days
Hackathons
Hackathons
Hackathons
January 2016 6 Functional Software Products 3 Days
HackathonsJanuary 2016 6 functional software products 3 days
Hackathons
Hackathons
In April, July, August and
October 2016
we built on
those projects .
Hackathons
Finding immunogenic peptides from single RNA-seq samples
DangerTrackDifficult to assess regions
Combined score is the average of SVs, mappability, GC..
NCBI region list
Encode blacklist
Get More Info!
In Twitter @NCBI@DCGenomics
In 2017 we will Build on Those Projects!
Biomedical Informatics Hackathon January 9th – 11th NIH Campus, Bethesda!
NCBI Genomics Hackathon March 20-22nd NIH Campus, Bethesda