Genomic Standards Committee Meeting Notes

By David LeBauer; ARPA-E TERRA Reference Data and Computing Team Comment

Participants

David LeBauer, Christine Laney, Michael Gore, Carolyn Lawrence-Dill, Eric Lyons, Noah Fahlgren

Agenda

Objective: review current status of pipeline and plans for first data release in November.

  • Introductions
  • Sequencing
  • Pipeline

Illumina Agricultural greater good initiative grant to Todd Mockler

A comprehensive understanding of the pan-genome sequence of this cereal crop will enable breeders to design and optimize their breeding strategies and improve grain sorghum yields … I’m grateful to Illumina for this opportunity to use next-generation sequencing to improve grain sorghum breeding because it’s essential to improving yields and enhancing food security in the developing world.” - Todd Mockler, TERRA Ref PI

Overview (Noah)

Sequencing

  • what has been done so far:
    • 192 resequenced genomes (~20-30x coverage each) from Steve K. bioenergy assoc. panel (BAP)
    • 192 additional samples sent to HudsonAlpha one week ago (20-30x)
    • External funding
      • Illumina grant to Todd Mockler for additional ~1000 sequences
      • DOE CSP for de novo
    • Data quality control and analysis to date done on the Danforth Center cluster
      • Trimmomatic => bwa => GATK => CNVator
      • By November: user will upload raw sequencing data and metadata to TERRAref pipeline using CoGe (below)
  • what is in pipeline
    • Raw data and experimental metadata added to Clowder
    • Clowder extractor
      • Upload data to the CyVerse data store (TERRA-REF)
      • Launch CoGe workflow using the API
    • Synchronize results back to Clowder/BETYdb

Clowder

  • Clowder: a database that can hold data of any format. Data being imported to clowder will automatically trip extractor that will move data to the correct location for discovery and analysis
  • Data will be uploaded to NCBI, SRA
    • Can we link from the SRA to CyVerse and Clowder easily and robustly?

CoGe pipeline

Downstream Analyses

  • GOBII
  • Other downstream tools?
    • SNP callling via CoGe
    • What is already within CoGe
    • Putting proprietary GATK on CyVerse (Mike G will send more info)

Data Sharing

  • when, where, and with what will we share as of November
  • Currently using CyVerse data store ( https://de.iplantcollaborative.org/de/)
  • Phytozome (a DOE database)- is this an appropriate for our data? Perhaps not for raw reads (Mike G)
    • Maybe we can submit variation information from the CoGe pipeline and update it as the reference genome is updated
    • Is Phytozome interested in hosting a pangenome resources?
  • NCBI SRA: raw data + experimental metadata
    • NEON has worked with SRA on data/metadata sharing, keep in touch with them
  • Others?

Other questions / ideas

  • How to get from genbank to related

NEON: providing metagenomic data, processed and made available to the public w/ mgrast; marker gene sequences will be hosted in SRA / not available w/in NEON portal but available from external repository. Genomic standard meeting next week, working on environmental soil meta-data package for Mixs http://gensc.org/mixs/submit-mixs-metadata/

NEON has started using EML to begin documenting sensor and observational data (currently online at http://data.neonscience.org but not pretty). May begin doing this w/ soil samples.

Action items:

Noah is leading the effort to run genomics data through using CoGe pipeline.

References

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