Finally, NCBI Genomes recognises Archaea*

I’ve been complaining about this for years. They fixed it. The NCBI have reorganised their genomes FTP site and finally, Archaea are not lumped in with Bacteria.

GenBank: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/
RefSeq:  ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/

Archaea are still included in the ASSEMBLY_BACTERIA directory; hopefully that’s next on the list.

[*] to be fair, they’ve always recognised Archaea – just not in a form that makes downloads convenient

How to: bulk retrieval of archaeal genome sequences from the NCBI FTP site

While we’re on the topic of mistaking Archaea for Bacteria, here’s an issue with the NCBI FTP site that has long annoyed me and one workaround. Warning: I threw this together minutes ago and it’s not fully tested.

Update July 7 2014: NCBI have changed things so code in this post no longer works