Report reference genome information for host genomes

[justinshaffer]

Hello!

I think it would be ideal to report the accession information for the reference genomes used for host filtering, including human. Currently the list of reference genomes provides links for direct downloads, however I think a link to the accession on GenBank or similar would be preferred or a good addition to this. Reporting the genome accession number at the very least should be required, as it is difficult to tell which assembly is being used for each host otherwise. Also, currently there is no download link / information for the human reference genome being used. This information could be provided along with the information about the microbial reference genome databases at the page below, or along with the links to download the genomes also at the link below.

https://qiita.ucsd.edu/static/doc/html/processingdata/processing-recommendations.html#shotgun-sequencing

Thank you!

[antgonza]

Remember, we do not support human sequences removal in Qiita; thus, no reference is available [*]. Now, with the link, could you figure out the accession of the other references? If yes, would you mind posting them here so I can add to the documentation?

Thank you!

[*] just to be clear, our internal SPP (Sequencing Processing Pipeline) does the human removal - not Qiita!

[justinshaffer]

Thanks for clarifying. Currently there is an option to remove several host genomes / artifacts that includes human, which is what I was referring to. I think if we include it there we should indicate which reference is being used. [image: Screen Shot 2023-03-06 at 11.55.26 AM.png]

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On Mon, Mar 6, 2023 at 10:43 AM Antonio Gonzalez ***@***.***> wrote: Remember, we do not support human sequences removal in Qiita; thus, no reference is available [*]. Now, with the link, could you figure out the accession of the other references? If yes, would you mind posting them here so I can add to the documentation? Thank you! [*] just to be clear, our internal SPP (Sequencing Processing Pipeline) does the human removal - not Qiita! — Reply to this email directly, view it on GitHub <#3264 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADSDCGCEFJWWEDLNZ754TYDW2YV6HANCNFSM6AAAAAAVRPSDCY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Justin Shaffer, PhD Postdoctoral Researcher Rob Knight Group Department of Pediatrics, School of Medicine University of California, San Diego justinshafferbio.wordpress.com

[antgonza]

Got it, that's a left over from a previous version and not actually available to select in that processing step. I think we should remove that option from the documentation.

[justinshaffer]

Makes sense. I agree. Thank you!

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On Mon, Mar 6, 2023 at 12:04 PM Antonio Gonzalez ***@***.***> wrote: Got it, that's a left over from a previous version and not actually available to select in that processing step. I think we should remove that option from the documentation. — Reply to this email directly, view it on GitHub <#3264 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADSDCGF6SUK3MUWMKVITQMLW2Y7MLANCNFSM6AAAAAAVRPSDCY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Justin Shaffer, PhD Postdoctoral Researcher Rob Knight Group Department of Pediatrics, School of Medicine University of California, San Diego justinshafferbio.wordpress.com