Sequences for BioProject PRJNA431646 not available online

[IgnatiusPang]

Dear Administrator,

I have tried to download the viral mock community (BioProject PRJNA431646) referenced in the VirMap paper. However, to the best of my knowledge it does not seems to be online (e.g. the data is not publically available yet?). If possible, would you please have a look at this for me? Thank you in advance.

Yours Sincerely,

Igy

[najami]

I'll look into it and get back to you.

…

On Thu, Jul 18, 2019 at 1:32 AM IgnatiusPang ***@***.***> wrote: Dear Administrator, I have tried to download the viral mock community (BioProject PRJNA431646) referenced in the VirMap paper. However, to the best of my knowledge it does not seems to be online (e.g. the data is not publically available yet?). If possible, would you please have a look at this for me? Thank you in advance. Yours Sincerely, Igy — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#8?email_source=notifications&email_token=AB2RWUL4FGU646FG5F2MJ6LQAAFAPA5CNFSM4IEXMGAKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G75NR4Q>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB2RWUNF6RFJAH6ZP2CCRXDQAAFAPANCNFSM4IEXMGAA> .

[QianGuoPKU]

Hi,
I wonder if there is any alternative access to the viral mock community sequence data. The data in NCBI seems to be unavailable still. Thanks.

[pcantalupo]

Maybe some of these might help you:

• NetoVIR Scientific reports paper 2015. See Table 1 of paper for list of 9 viruses that were combined together. SRA link.
• Scientific reports paper table 3

Good luck

[najami]

NetoVir is a good set and we ran it through VirMAP as well - thanks for suggesting this @pcantalupo. This recent paper also cites a few mock communities and virome datasets:

Sutton, T. D. S., Clooney, A. G., Ryan, F. J., Ross, R. P., & Hill, C. (2019). Choice of assembly software has a critical impact on virome characterisation. Microbiome, 7(1), 12. https://doi.org/10.1186/s40168-019-0626-5

I've contacted NCBI and requested BioProject PRJNA431646 to be made public. I am not sure why this hasn't been public since the paper came out but we'll get it out there so @QianGuoPKU, @IgnatiusPang, and others can use it. Please let me know if there is anything else I can help with in the meantime.

[pcantalupo]

@najami Thank you for the Sutton link!

[QianGuoPKU]

@najami @pcantalupo Thank you.

[najami]

@pcantalupo @IgnatiusPang @QianGuoPKU - we (re)submitted the dataset to SRA. I'll let you know as soon as it is available.

[IgnatiusPang]

Thank you for re-submitting the data!

[najami]

@IgnatiusPang you are welcome!

Here's the direct link in case others are interested:
https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR9875293