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Report reference genome information for host genomes #3264
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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! |
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]
…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!
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Justin Shaffer, PhD
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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. |
Makes sense. I agree. Thank you!
…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.
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Justin Shaffer, PhD
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Rob Knight Group
Department of Pediatrics, School of Medicine
University of California, San Diego
justinshafferbio.wordpress.com
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fix #3264 + processing_job email subject
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!
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