Moore Notes 7 2 14

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Group call

  • Participants: Katie, Jonathan, Tom, Patrick, Stephen, Sarah
  • MMI virus ecology forum RFP
  • Tom: what scientific societies to join?
  • Eukaryote detection
    • Dongying is trying to expand the eukaryotic marker set
      • e.g., diatom markers
      • Need many so they are sequenced in metagenomic data (due to large genomes, which mean lower coverage)
    • Patrick also wants to figure out which reads are eukaryotic (for gene families present in all domains of life)
  • Pollard lab summer intern: Krista Kernodle
    • Total OTU diversity of Central Park (with Josh)
    • Strain level variation in gene presence/absence (with Stephen)
      • Jonathan: try mapping reads to multiple reference genomes
      • Also looked at metaref marker/pan/core classifications
      • Phylogenetic analysis is better than presence vs. absence
  • Shotmap
    • Core development of code is closed
    • Validation on Gladstone machines went well
    • MetaHIT vs. multiple dbs
    • Stephen re-running all simulation experiments and analyzing results
    • Might release simulation pipeline code with paper
    • Manuscript draft in progress
    • Jonathan: Is there a consensus on how to do metagenomic annotation?
      • MG-RAST is commonly used, as a black box
      • Humann for KEGG
      • We should evaluate their default settings versus shot map (on simulated data)
  • Upcoming calls
    • July 9: No call
    • July 16: Shotmap & Dongying marker genes
    • July 23: Krista