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Thank you for writing this tool, it has been a huge help to me!
I have a quick question regarding the downloading of assemblies. I'm attempting to download assemblies based on taxids -- which works great, but I would only like to download one assembly per species. I am aware of the --refseq-category command that will help in this regard (i.e. just representative or reference), however, some species do not have 'references' or representative assemblies (e.g.https://www.ncbi.nlm.nih.gov/assembly/GCF_003030345.1/ )
Is there some way I can download these even if they don't have references/representatives?
Thanks!
Raphael
The text was updated successfully, but these errors were encountered:
Hi Raphael,
Unfortunately, there's no straightforward way of doing this. How do you pick which assembly is the one you want if there's a thousand assemblies?
Also keep in mind that the species are occasionally not assigned correctly.
@EisenRa You can parse the assembly summary file, group accession IDs together that have the same species tax ID, then feed those IDs to ncbi-genome-download with the -A option. That would work if you don't care which one you download.
Repository owner
locked and limited conversation to collaborators
Mar 21, 2022
Dear authors,
Thank you for writing this tool, it has been a huge help to me!
I have a quick question regarding the downloading of assemblies. I'm attempting to download assemblies based on taxids -- which works great, but I would only like to download one assembly per species. I am aware of the --refseq-category command that will help in this regard (i.e. just representative or reference), however, some species do not have 'references' or representative assemblies (e.g. https://www.ncbi.nlm.nih.gov/assembly/GCF_003030345.1/ )
Is there some way I can download these even if they don't have references/representatives?
Thanks!
Raphael
The text was updated successfully, but these errors were encountered: