How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
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2.1 years ago
O.rka ▴ 720

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.

metagenomics accession ncbi taxonomy database • 1.0k views
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2.1 years ago
vkkodali_ncbi ★ 3.7k

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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Incredible, thank you so much.

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