wuhCor1 metadata for countries

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Mike Honey

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Jul 6, 2021, 1:43:39 PMJul 6
to gen...@soe.ucsc.edu

Hello,

 

I came across this resource on your site:

http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2//

 

I’m interested in blending the metadata for those sequences into this dataviz project – a volunteer effort to try to present data on this important topic to a non-technical audience:

https://github.com/Mike-Honey/covid-19-genomes#readme

 

It’s been quite straightforward to download and ingest your data – thank you for that.

 

But now I examine it, its seems the data for most countries is out-of-date (besides, US, UK and Bangladesh).  For example via outbreak.info etc I can get sequencing stats for Australia up to late June. But in your metadata file it seems the latest available is October 2020?

 

Thanks

Mike Honey
Technical Lead
Manga Solutions

Mobile: +61 412 235 469
E-mail:
mike....@mangasolutions.com
Web:
www.mangasolutions.com

 

Brian Lee

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Jul 6, 2021, 9:01:06 PMJul 6
to Mike Honey, gen...@soe.ucsc.edu
Dear Mike,

Thank you for using the UCSC Genome Browser and your question about wuhCor1 metadata for countries.
  
When looking at the at GenBank sequences from Australia using NCBI Virus and order by collection date (not release date), it does look like Oct. 2020 is the latest information: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049&Country_s=Australia The outbreak.info site has access to the GISAID database, which is the most comprehensive collection of SARS-CoV-2 genomes, but GISAID does not permit bulk download files to be made public. Our public download files are generated from sequences in fully open repositories (GenBank, COG-UK and the China National Center for Bioinformation), that don't have such restrictions. Our sequences from Australia are all from GenBank.
  
It may be worthwhile to reach out to the authors of the most recent Australian GenBank sequences (Seemann,T., et al.), to ask why they stopped submitting to GenBank.

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

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Mike Honey

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Jul 7, 2021, 11:41:08 AMJul 7
to Brian Lee, gen...@soe.ucsc.edu

Hi Brian,

 

Thanks for the reply, that all makes sense to me and was very useful info.   

 

I will try and encourage the Australian contributors to continue – I think fully open repositories are best and should be supported. It looks like Seeman,T is currently an A/Prof at a university that is a client of mine, so I’ll try to encourage him to continue.

https://findanexpert.unimelb.edu.au/profile/704966-torsten-seemann

 

Regards

Mike

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