Moore Notes 7 2 14

Group call

• Participants: Katie, Jonathan, Tom, Patrick, Stephen, Sarah

• MMI virus ecology forum RFP

• GBMF evening with marine microbiologists
  • July 30
  • Tech Museum in SJ: http://www.thetech.org/

• 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