Moore Notes 2 9 15

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Group Call

  • Participants: Katie, Jonathan, Tom, Stephen, Guillaume, Dongying, Ladan, Stacia, Patrick, Josh
  • Upcoming meetings
    • JGI users meeting
    • ASM in New Orleans
    • AAAS this week (Katie speaking at main meeting, and citizen science satellite meeting)
  • MicrobeCensus changes have been pushed recently
    • Tom will check affects on ShotMap
  • ShotMap final loose ends
    • Target this Friday for these
    • Submit a week or so later
  • Tara Oceans update
    • PATRIC genomes as reference db
      • JE: check for phylogenetically novel genomes
    • Genome clusters
    • Gene clusters within genome clusters
    • DIAMOND for read alignment
      • Faster than RAPSEARCH2 with a lot of reads
      • A lot of compute is indexing of huge protein db
    • Josh working on prioritizing using environmental variables
  • Stephen: Strain variation in gene copy number in metagenomes (slides)
    • Used PhyEco markers to identify genome clusters
      • Bacterial specific markers perform best (Bacterial and Archaeal are probably too conserved)
      • Ribosomal proteins have high sequence conservation (too high? maybe due to codon bias?)
    • Perpetual updating
    • Discussion of this paper: http://www.cell.com/cell/abstract/S0092-8674(15)00013-6
      • JE: how does this relate to mapping errors (e.g., repeats)?
      • Future directions for Stephen given this paper
        • They did not generate methods that are easily used by others
        • Create data resources (e.g., genome clusters, pangenomes)
        • Analyze more data, better data
        • Use genes outside KEGG
        • Look at SNPs
        • Unanswered biological questions: Co-variation of genes (genomic islands), biogeography, core genes, gene flux across species
        • JE: Look more broadly at covariation of genes (present/absent, not just copy number variation)
      • Applications to metatranscriptome analysis, "phylogenetic RNA-seq"