Moore Notes 2 13 13

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Group Call

  • Participants: Katie, Tom, Stephen, Josh, Guillaume
  • In-person meeting
    • Date: June 17 (Mon) with June 19 (Weds) as backup, one day meeting no overnight
    • Location: tentatively SF
  • Guillaume will visit SF soon
  • SFams automatic updates
    • Tim Laurant will work on the QC side of the update pipeline
      • Precision and recall, network assessment, etc for new families
      • Will stitch together existing software into a pipeline for computing these metrics
    • Apply to all families at each update
      • Big compute as db grows, might need to improve efficiency
      • But maybe not - can run in background
    • Stephen's additional QC metrics
  • LAST vs. BLAST for classifying reads into families (MRC, phyloSift)
    • After partitioning reads by genomes, looks like BLAST is better for diverse genomes
    • LAST is a lot faster though
    • For phyloSift could double check long branches with large m parameter or fixed length seed or several m's
    • Similar to TribeMCL
  • Next week: Katie teaching