COVID-19 Records

Chat message

Slack / Private Message Drop, p.545 [SLACK_000759] · slack_pm:msg:05685

Page text: p.545 · original PDF

Date
2021-02-24 09:29
Type
chat message · slack
recipient
Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker
Kristian G. Andersen

Recipients on this medium are inferred from channel membership, not per-message addressing.

If this is from NYC, it's possible they used Illumina's DRAGEN pipeline

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

  1. 2021-02-24 09:27 Robert F. Garry open
    Speaking of the WSJ - they just requested an interview to discuss our Virological post.
  2. 2021-02-24 09:27 Andrew Rambaut open
    It is weird the V701A reverting in the S477N lineage - maybe the tree is wrong
  3. 2021-02-24 09:29 Robert F. Garry open
    HMMMM - that is interesting.
  4. 2021-02-24 09:29 Kristian G. Andersen open
    Oh... We have identified a MAJOR issue with Illumina's consensus caller - it's calling reference calls if there are _any_ mismatching reads at a variant site. That might be why
  5. 2021-02-24 09:29 Kristian G. Andersen
    If this is from NYC, it's possible they used Illumina's DRAGEN pipeline
  6. 2021-02-24 09:29 Kristian G. Andersen open
    (I have reached out to them - crickets).
  7. 2021-02-24 09:30 Kristian G. Andersen open
    shared file(s): image (1).png, Screen Shot 2021-02-24 at 09.30.29.png
  8. 2021-02-24 09:34 Andrew Rambaut open
    Interesting - we have seen quite a lot of 'reversions' in some of the VOCs. Who would be using this consensus caller? Is there a way to find out?
  9. 2021-02-24 09:34 Kristian G. Andersen open
    Preprint on the NYC sequences - pretty interesting. https://www.biorxiv.org/content/10.1101/2021.02.14.431043v2.full.pdf

Full conversation →