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Slack / Private Message Drop, p.546 [SLACK_000760] · slack_pm:msg:05690

Page text: p.546 · original PDF

Date
2021-02-24 09:34
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.

I'm worried A LOT of people are using the Illumina pipeline - and there's no way to find out in most cases

In context

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

  1. 2021-02-24 09:29 Kristian G. Andersen open
    (I have reached out to them - crickets).
  2. 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
  3. 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?
  4. 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
  5. 2021-02-24 09:34 Kristian G. Andersen
    I'm worried A LOT of people are using the Illumina pipeline - and there's no way to find out in most cases
  6. 2021-02-24 09:35 Kristian G. Andersen open
    Any lab that hasn't previously been involved in virus sequencing and isn't as comfortable with command line tools would likely use this caller. It's a big big problem.
  7. 2021-02-24 09:46 Kristian G. Andersen open
    B.1.526 with S477N: https://outbreak.info/situation-reports?country=United%20States&division=California[...]1.526&muts=S%3AS477N&selected=New%20York&selectedType=division
  8. 2021-02-24 09:47 Kristian G. Andersen open
    Interestingly, none with both (kinda supporting this is a real effect - since they're independent events): https://outbreak.info/situation-reports?pango=B.1.526&muts=S%3AE484K&muts=S%3AS477N

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