Moore Notes 8 6 14

Group Call

• Participants: Katie, Tom, Stephen, Patrick, Stacia, Dongying, Sarah, Guillaume

• META Symposium
  • Talk summaries, stately

• Sharpton lab
  • New postdoc: Chris Gaulke (from UC Davis)
  • Students

• Shotmap authorship discussion

• Stephen: slides
  • Simulation framework for evaluation of gene family relative abundance estimates from shotgun metagenomes
  • Mock communities with species abundance distributions from Bork/Weinstock paper
  • Translation methods affect performance and data volume/compute
    • Metagenomic gene prediction methods reduce data volume a lot and perform almost as well as six-frame translation
  • Comparison with MG-RAST
    • Shotmap annotates more KOs
    • Abundance estimates are correlated (on log scale), but there is disagreement
    • Working on annotating genomes in the simulation to have a gold standard for comparison
    • Suggestions: color by KO properties, quantify and then eliminate not-detected KOs
  • Other parameters evaluated:
    • Sequencing depth
    • Search method
    • Score threshold (versus e-values, which are >0 for huge dbs)