nature of GISAID's 700+ datasets

[Ramón Fallon]

I know I'm not alone in thinking that GISAID seems to be ahead of the

curve, especially in terms of datasets.

It's possible to download the newick trees, that's all well and good. The raw

data is not (some what expected, mind you), Just thought somebody here might know

answers to following questions:

1) Do registered users get access to the raw data (I have my doubts)

2) How is the raw data from such diverse sources uniformized?

3) which format are most of the labs submitting their data as? (I bet it won't be what the

 what the Treetime/Augur/Auspice pipeline wants ... if bioinformaticans didn't have to convert file

format, 50% of their job would be gone. :-D)

Thanks in advance!

[Rutger Vos]

As a registered user you have access to metadata about individual cases, in PDF format, and to assembled viral genomes in FASTA format.

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Met vriendelijke groet,

Dr. Rutger A. Vos

Researcher / Bioinformatician

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[Ramón Fallon]

Many thanks for your reply Rutger.

Unfortunately, no registration accepted for me.

[Pjotr Prins]

On Wed, Mar 25, 2020 at 01:23:15PM +0000, Ramón Fallon wrote:
> Many thanks for your reply Rutger.
> Unfortunately, no registration accepted for me.

What did you try? Any reason given?

Pj.

[Ramón Fallon]

Thanks for interest Pjotr.

"As yet" I should have added. I.e. Tried on Sunday, no reply.

Used a commercial company email (to avoid gmail- nor yahoo- email addresses delays).

[Pjotr Prins]

On Wed, Mar 25, 2020 at 01:40:21PM +0000, Ramón Fallon wrote:
> Thanks for interest Pjotr.
> "As yet" I should have added. I.e. Tried on Sunday, no reply.
> Used a commercial company email (to avoid gmail- nor yahoo- email
> addresses delays).

Let's contact them and see if we can get a biohackathon account. Also
we should inform them about our plans and needs. We should give them a
chance to play with us before we ignore them altogether.

Anyone here wants to take the initiative? Anyone already has a contact
with GISAID?

Pj.

[Rutger Vos]

I have had an email exchange with them but, as I said, they were a bit touchy. I might not be the best person to try again, though I'm willing if nobody else is closer to them.

It might be worth reading some of the issue threads for nextstrain (e.g. this one) to get a feel for the capriciousness of GISAID at this time. It sounds like at least the following is happening:

1. they're slow to process account applications
2. they turn the download button on or off on an individual basis

It would be good to know what their problem is, so to speak. Is this just policy? Perhaps they can then be convinced to change it? If the problem is technical (e.g. they don't have the bandwidth to share with everyone) then perhaps we can help them allocate resources?

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[Ramón Fallon]

Thanks Pjotr and Rutger for comments and info. Helps shed light!