Chat message

Slack / Private Message Drop, p.135 [SLACK_000349] · slack_pm:msg:01383

Date: 2020-08-14 14:51
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut

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

The issue here is that this is NextStrain's 'Oceania' site. This has a focus on Oceania genomes and down-samples the rest of the world which means it will over sample Australia.

In context

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

2020-08-14 14:32 Kristian G. Andersen open

You bet - definitely worth an extra (careful...) look. They made some conclusions on our Baja / SoCal sequences that are definitely not correct though, so something tokeep in mind (in this particular point, it's impossible to say whether the virus moved South (as suggested), North, orfrom some completely different location). [shared file(s): Screen Shot 2020-08-14 at 2.29.40 PM.png]
2020-08-14 14:32 Edward C. Holmes open

My money is on NextStrain screwing it up.
2020-08-14 14:32 Kristian G. Andersen open

And just for reference - here's the wording from our own report [shared file(s): Screen Shot 2020-08-14 at 2.32.03PM.png]
2020-08-14 14:33 Edward C. Holmes open

Bloody Trevor.
2020-08-14 14:51 Andrew Rambaut

The issue here is that this is NextStrain's 'Oceania' site. This has a focus on Oceania genomes and down-samples the rest of the world which means it will over sample Australia.
2020-08-14 14:56 Kristian G. Andersen open

@Eddie Holmes And they don't check to see if these genomes are shared outside Australia? For that types of question, one really needs to look outside the sandbox... (this reminds my of the ever-occurring issue of people taking short reads and blasting them against viral databases to conclude that they have viruses in their samples... Only to realize later that they are human reads).
2020-08-14 15:36 Edward C. Holmes open

Yes, that's my guess.
2020-08-14 15:37 Edward C. Holmes open

I will be criticising NextStrain if so. I'm just checking with the Melbourne people now.
2020-08-14 15:44 Edward C. Holmes open

@Eddie Holmes Pretty incompetent analysis. I'm going to enjoy this.

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