NCBI taxonomy mapping file 2023

News & Announcements Updates and Changes
#1

Dear Daniel,

approx. when will be available a recent (2023) protein/nucleotide accession to NCBI-taxonomy mapping file?

Thank you in advance for any news:

Best regards: Balázs

#2

Hi Balázs,

If you only need the taxonomy classification, I regularly update the megan-map.db with the prot.accession2taxid file from NCBI using sqlite3 UPDATE for existing accessions and INSERT for new accessions.

Best,
Greg

#3

Hi Greg,

I would really appreciate it if you could provide the updated megan-map.db file, because although it is very cumbersome with the diamond 102 format and Megan custom ncbi.map / ncbi.tre files (after CSV import), and it might not work with the huge tabular files at read level (I’m trying to do it at contig level). Anno I read Daniel’s post on this, but unfortunately I’m not yet familiar with database programming, it would save a lot of time. Oh and yes, I’m only interested in the taxonomy class. part :slight_smile:

Thank you very much: Balázs

#4

I’ve spent the whole week on this and wasn’t able to update everything… So now I’m aiming to at least make a new mapping database available for the NCBI taxonomy.

1 Like
#5

Dear Daniel,

Many thanks in advance!

B