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

1 Like
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.

3 Likes
5

Dear Daniel,

Many thanks in advance!

B

6

Many thanks! I am looking forward to it as well. I have observed scenarios where reads were assigned to an unexpected species, only to find instances of proteins in the assigned species (via the “Show Alignment” tool) had accession numbers that actually belong to the expected species according to the NCBI database. I was using megan-map-Feb2022.db and a download of the NR database just a couple of weeks ago.

Appreciate the effort!

7

Dear @Daniel,

I was wondering if there was any update to the taxonomy database? The only one I can find in the downloads is the Feb-2022 one. I’m struggling with a highly diverse rumen community of cows from which the updated db would be extremely valuable.

I appreciate the help.

  • HM