i5K Coordinating Group

Conference Call Agenda

October 21, 2020

11:00-12:00 (EDT)

Attending: Mark Blaxter, Rob Waterhouse, Monica Poelchau, Duane McKenna, Surya Saha, Jay Evans, Marian Goldsmith, Brian Sheffler, Mara Lawnicziak, Stephen Richards, Sue Brown, Kristen Panfilio, Anna Childers, Robert Miller, Brad Coates

A partial recording of this meeting is available on request.

  • Meetings
    • Biodiversity Genomics/EBP recap
      • Great job, Dorith and Surya!
      • Poster session on zoom instead, with 3-4 minute spiel per poster.
      • 3,200 people registered - 5,400 different people logged in! 90 countries participated.
      • Statistics will be sent for the i5k session
      • Please fill out the questionnaire
      • Speakers should have received a request to put talks on youtube permanently
      • Recordings should be available on site for 1 month. If the # of people viewing them is still high after 3 weeks, they may extend for another month
      • Pre-recorded talks went well, having live questions was good
      • Kudos for the AV support received!
      • Slack also helped for troubleshooting and networking
      • Talks made apparent the need for funding for genome projects…
      • Questions about technologies to use and costs
      • Thoughts on hybrid meetings in the future? The organizing committee is already discussing this - satellite meetings in different countries discussing the same content. In-person meetings in future will probably look quite different after this experience - they are still necessary for better cross-talk (people who wouldn't talk to each other otherwise). This cross-talk could help groups that aren't already part of existing sequencing groups (e.g. VGP, i5k) to join in.
      • Virtual meetings also harder for younger people/those not established in a community to start networking (e.g. the random connections you make at meals)
      • Manual genome assembly curation (using GVAL program, https://www.biorxiv.org/content/10.1101/2020.08.12.247734v1) - 100 or so manual corrections per Gb of assembly usually necessary
      • Kristen: How do people feel the diversity aspect went? taxonomic, regional, and otherwise?
        • EBP, VGP, GiGA, Dtol organized. Biodiversity - Each taxonomic group had a session.
        • Lower/middle income countries: 90 countries attended. Fora were held with panelists. EBP Africa had a showcase- there was a lot of discussion on how African scientists can contribute
        • Early career scientists: Forum was held with panelists.
        • 'Challenges' presentation at the end of the meeting also added some diversity to the dialogue
        • Peter Dearden gave a very thorough overview and discussion on how to sequence a native flora (not just sequencing, but also involving the local community)
      • When do you need a VGP - quality assembly? Mark's take on this is that if we can, we should. Of course not every project needs a high-quality genome. The cost is getting low enough and the technology good enough where this high standard can be feasible (to enable answering more questions). Anna - why do it twice when you can do it once? fringy: we are working against this question all the time. Perhaps we need to foster more of a 'reference dataset' mindset. Mark and Sue: Even conservation genomics might need high quality genomes, they just don't know it yet.
  • ESA Nov 15-18, 2020 (Monica, Brad)
  • All talks recording/recorded
  • Still need to work on the panel session - looking for input on how to make this discussion session work. Anna - best to focus on bigger-picture questions. Rob- cf. the Biodiversity genomics 'challenge' session. Speakers prepared a 2-minute blurb ahead of time. One way to get the conversation to a higher level.
  • Panel Session - advertise time and date of this (the rest of the talks are all on-demand) use ArtGen Slack
  • Friday, November 20, 2020 11:00 AM – 12:00 PM EST

    • PAG-San Diego: Ag100Pests Talks Jan 9-11, 2021 (Anna, Surya)
      • postponed until March, more information tbd. Hard to know whether to plan or coordinate anything yet.
  • Project Database (Mark, Mara, fringy, Monica): ENA-based
    • DToL: ~24 species a week, some lag to get into public databases. Genomes are coming out beautifully. \>600 species in freezers. 246 in sequencing. Look at Mark's slides for the details
    • https://tolqc.cog.sanger.ac.uk/index.html - open portal for QC data for all read sets
    • https://goat.genomehubs.org/preview/ - genomes on a tree. This may be able to stand in for a 'status' website (e.g. lab x is working on species y, current status is z). Written by Richard Challis and Sujay Kumar, uses elasticsearch
    • EBP sub-committee has draft documents ready, but still a bit more work to get it close to finished, Mara noted we need some more cross-talk across the groups especially before anything goes online
  • Project Updates - Bees (Brian).
    • Some bees are working - these have been difficult to extract. It seems that the longer the material is stored, the worse the DNA quality (in general). Bees are worse.
    • Mara: they've been able to extract several hymenoptera. 2 wasps are having trouble completing the genome, though, even though the underlying data are sound. Perhaps a chromosome structure issue (B chromosomes)? Can also check protocols on ATUTA slack.
    • Lot number issues for PacBio supplies?