How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
I'm trying to figure out how to go from genbank assembly identifiers to their taxonomy identifier in NCBI.
Is there a flat file I can download somewhere? Nothing seemed to do the trick here: https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/
If possible, I'd rather not download an R package that does this but if that's the only option then that's fine.
1 answer
The assembly_summary files located in this FTP path have this information: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS
Specifically, you should look at the file assembly_summary_genbank.txt
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