Moore Notes 1 23 13

Group Call

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

• Guillaume: SFams updating
  • Had issues downloading some genomes
    • Probably due to webserver being down
    • Might always have to do some by hand (e.g., very large genomes)
  • Insertions into db are slow (5 million so far)
    • Tom might have a solution for doing bulk inserts into MySQL
  • Problems with LAST jobs on UCD cluster (too many sequences going through at one time?)
    • Will also run BLAST
  • Got round 2 genomes data with renamed families from Tom
  • Set up github repository for updating code: https://github.com/gjospin/Sfam_updater

• Stephen: tuncated SFams
  • Due to errors in IMG's gene prediction pipeline?
    • Can this hypothesis be confirmed?
    • Updated genomes might have improved annotations
  • Could also be due to real truncated proteins (e.g., due to frame shifts)
  • Annotate them in some way (merge, clans, notes)
  • Guillaume did an analysis of truncated sequences - cross reference with Stephen

• Josh: contacted Jack Gilbert
  • He's interested in being involved in beta-diversity niche mapping
  • Wants to set up a time to talk one-on-one
  • Working with earth microbiome data (lots of 16S data)
  • Will ask if he is doing shotgun metagenomic sequencing (e.g., English channel)

• Tom: read classifier project
  • Software development mostly done
  • Stephen did statistical analysis of performance
  • Starting data analyses
    • Data set of a free living (e.g., marine) community with lots of novel lineages?
    • Tanya Wojcicki at JGI
    • Look at where new genomes are coming from in IMG (mostly GEBA, lost of cyanobacteria)

• Jonathan: setting up website on Wordpress

• Katie: speaking about metagenomics at Brilliant Science Cal Acad event this week

• In person meeting in Davis
  • Audrey will do a doodle poll

• Moore foundation meetings - Jonathan at one, Katie at other

• Progress report was submitted and receipt confirmed