i5K Coordinating Group

Conference Call Notes

June 17, 2020

11:00-12:00 (EDT)

The focus will be organizing July's virtual meeting. Updates only as needed.

Attending: Sue Brown, Surya Saha, Jay Evans, Mara Lawniczak, Chris Childers, Kristen Panfilio, Kevin Hackett, Robert Waterhouse, Monica Poelchau, Anna Childers, Glenn Hanes, Bob Miller, Robert Nowierski, Stephen Richards, Robert Melis, Brian Scheffler, Xinhai Ye

Move to Zoom?

  • Meetings
    • Virtual AGS (Rob, Sue): _ July Meeting _
      • @ 16:55 CH time 17th June, 27 replied positive, 3 replied negative, 34 no email reply only info from Gform
      • 20-24 July - exact dates TBD (21/22/23 or 22/23/24 depending on workshops)
      • 4-5 speakers per session over 3 days
      • Informal poster display using slack
      • Web page at i5k github site
      • Jitsi mini chatroom meeting via slack
      • Record talks for youtube channel and post slide deck as long as speakers agree
      • Next vAGS meeting on Tuesday June 23rd to decide speakers per session
      • Questions via the Q&A function in zoom webinar
      • Possible workshop(s) after the vAGS meeting for EuPathDB and i5k annotation
      • Follow up workshops from Terrence NCBI team
    • ESA-Orlando (Monica, Brad)
      • Virtual meeting, format TBD
    • PAG Ag100Pests Talks (Anna, Surya)
    • BioDiversity Genomics meeting (Mara)
      • Free and virtual meeting
      • Parallel sessions and breakout groups
      • Survey (for PIs) closing tomorrow
  • Project Database (Mark, Mara, fringy, Monica): ENA-based
    • Probably going to team up with DToL more closely as they seem to be more advanced with their progress
  • Project Updates
    • EBP Update (fringy)
      • EBP meeting tomorrow morning
      • Informatics focus for tomorrow's meeting
      • Labs coming out of hibernation slowly
      • 100 CA ecosystem species have been chosen with \<10 arthropods (spiders)
      • HIFI reads have improved assemblies drastically without a major cost impact. Saving money on AWS compute costs
      • ONT reads to compete with HIFI will be interesting but to products yet
      • Ag100Pest can help formulate DNA extraction guidelines (Anna, Brian)
    • DToL (Mark, Mara)
      • Back in the lab, a lot of arthropods coming through, are happy to 'send' a speaker to vAGS
    • Ag100Pests, include Desert Locust (Anna)
      • funding received for genome and transcriptome
      • Coordinating with [someone] who's doing 6 locusts?
      • Murder wasp: sample from colony received, PacBio done and pretty good assembly, highly repetitive
      • Good on tiny insects you can see, once so small that you cannot see them then results are not so good
      • Releasing genomes to NCBI in June
      • Spending less than $5k per genome for genomes smaller than 1Gb if we need only 1 SMRT cell. Cost is only for consumables. No cost for personnel and compute
    • Beetles (Duane)
    • Cornome (Brad, Jay, Dave)
      • Jay: keeping beneficial insects safe in corn fields
      • 5 species coming along
      • Minute pirate bug
      • Pacbio, ONT and Illumina data for 5 species available now
      • Brian: Might need to redo the assembly with only HIFI reads
    • Bees (Brian)
      • Process in place to get things moving with Scott Geib
    • France (Denis)
    • California Ecosystem (fringy) - species are being chosen, but not many arthropods so far (fewer than 10) - there is a focus on popgen type design: 150 species plus 100 individuals per species. Brian: 20-30% reads were non-plant when seeds were not sterilised!
  • Expanding the Membership on the i5K Steering Committee (Rob)
    • send new member suggestions to Kevin H.
  • I5K Webinar Update (Anna): Merge this with the i5K Steering Committee Meeting?
    • 'extra' talks from vAGS could be offers slots on i5k Webinar series
  • New Funding Ideas
  • Monica: Identification of contamination in assemblies from raw reads in SRA for false positive LGTs. Add metadata about the kinds of DNA run on the sequencer
  • Future i5k coordination meetings on zoom (Monica,Kevin)

NEXT MEETING: July 15, 2020

11:00-12:00 am EDT