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
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
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
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
Thank you very much: Balázs
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.
Dear Daniel,
Many thanks in advance!
B