Moore Notes 4 3 13

Group Call

• Participants: Katie, Tom, Guillaume, Dongying, Josh, Stephen

• Marine niche mapping paper published in ISME Journal: http://www.nature.com/ismej/journal/vaop/ncurrent/abs/ismej201337a.html
  • Does the new data downloaded from CAMERA have a broad enough geographic/environmental distribution to do protein family niche modeling?
  • Josh & Guillaume will look into this
  • Tom: what data QC do we need to do?
  • Prioritizing data sets to process (at least until we can go over to Google)

• Tom: MRC
  • Ready to process data
  • Infrastructural bottlenecks
    • 24 hours per Illumina data set if at full capacity on the QB3 cluster
    • Shared NFS mount between cluster and data server needs to be modified to allow more simultaneous hits
    • Other compute resources? Merlot, Google, new IHG cluster, OSU (next Fall, tentative)
  • Dongying: What method is being used for read search?
    • Default: RAPSEARCH
    • Others implemented: BLAST, LASTALL, HMMSEARCH, HMMSCAN

• SFams updating
  • Guillaume will update repo
  • Tom will launch job
  • Tim L working on QC and functional annotation of families
  • Next: clan definitions
  • Dongying: How do I search only a subset of families? e.g.,
    • With >5 members
    • High quality

• Katie: Janelia conference
  • Sean Eddy's idea about information content of profile models
    • Entropy scaling (default = 6) may be inappropriate for short reads
    • Stephen: fragthresh parameter handles query as fragment if <50% of target model, but does penalize if >50% (solution: set parameter to 1.0)
  • Tandy Warnow's SEPP
    • Divide-and-conquer approach to speed up pplacer and similar methods
    • Applications
      • Taxonomy identification of short reads (TIPP)
      • Building huge alignments (UPP)
  • Richard Durbin's suggestion to think about Ferragina-Manzini (FM) index to speed up MRC
    • Based on Burrough's-Wheeler transform, related to suffix arrays
    • Previously used for aligning short reads to genomes (BWA, Bowtie)
    • Recently applied to assembly (extension of SGA assembler, really sped it up)

• Federico Lauro's Indian Ocean cruise
  • Ask Jonathan next time