NCBI DB and Taxonomy classification
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Entering edit mode
7 weeks ago

Hi, I'd like to perform a taxonomic classification (not only of microorganisms but also of all Eukaryota) of shotgun output sequences with megan6, which requires to download a reference db with sequences or genomes to compare. I was looking for something usefull in the Index of /blast/db (nih.gov) site but I couldn't understand the differences between some file such as:

Does anyone know if they are the same DBs but merged in the FASTA subdir?

Can somebody give me some help and/or advice to complete my task?

Thank you very much

Giulia

db.NCBI taxonomic taxonomy • 238 views
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Entering edit mode
7 weeks ago
GenoMax 127k

Files in FASTA directory are just fasta format files for nt.

You should download the pre-formatted database files (all nt pieces) from https://ftp.ncbi.nih.gov/blast/db/.

To do taxonomy based searches you will also need a companion taxonomy database set of files. They are in the directory above with basename taxdb*. Download and have them available in the same folder as your nt files.