Moore Notes 5 8 13

Group Call

• Participants: Katie, Jonathan, Tom, Stephen, Ladan, Guillaume, Dongying

• JE: Invited to Ed DeLong metagenomics meeting in Catalina (NSF)

• SFams updater
  • Tom & Guillaume have finished updater code
  • Tim L has done the QC code and functional annotation code
    • No help yet from JGI regarding annotation files
    • So doing our own annotations
  • Job with new genomes (>2000) will be launched in two weeks
  • JE: what about contigs from environmental samples and not just genomes?
    • Tom: talked to C. Titus Brown, who thinks this is possible
    • Would have to modify some of automation workflow (e.g., outside IMG)
    • JE: BAC and cosmid sequences
      • Tom: let's work on this after the current update, e.g., for next paper
    • Tom: what about assembled metagenomic genomes (e.g., IMG MG)?
  • Stephen: need to be cautious about seeding families with truncated sequences
  • KP: Discuss at June 17 meeting

• Niche mapping of protein functions in soil data (with Jack Gilbert)
  • Continental US samples
  • Tom: If ecologically diverse, should we work on this?
  • Josh will follow up on marine samples
  • Stephen: misclassification could be a problem
  • Tom: more diverse communities means

• Josh: global diversity estimation

• June 17 Meeting
  • Logistics
    • Start time? 10am
    • Lunch in
    • End by 5pm
  • Organization of presentations
    • Code: MRC, sims, diversity mapping, simulations, phylogenetic OTUs
    • Data: SFams new release, classification outputs of metagenomes (e.g., English Channel)
    • Analyses: Maps, English Channel results, simulation results, maybe phylogenetic OTUs on genomes
    • Brainstorming sessions on specific topics: SFams new features, merging MRC with PhyloSift, accurate relative abundance of protein families

• Progress report text due to Katie by May 26th at latest