Francisco Latorre

I had the same issue: using `conda install -c bioconda coverm` would install version 0.4.0 by default, and installing version 0.6.1 raised an error. However, I stated the order of...

For the taxonomy database of MMSEQS2 you need the taxdump files: names.dmp, nodes.dmp, taxid.map, delnodes.dmp & merged.dmp A few weeks ago I tried creating the taxdump files using taxonkit's function:...

First, you create the database as `mmseqs createdb sequence.fasta sequenceDB` with the reference fasta. Then: `mmseqs createtaxdb sequenceDB tmp --ncbi-tax-dump ncbi-taxdump --tax-mapping-file taxidmapping` `ncbi-taxdump` and `taxidmapping` are the files that...

Yes, exactly like that! The taxidmapping file is the taxid.map that taxonkit creates. Looks like this; ``` e66f926af8418c8873d264785662420e 236192150 38c6e6957eabc901ba3b9c708a5e2eee 236192150 083441fc54d5eb9ecc0cd83490139b14 1443417319 5df8df7ddea8c8316cfdfc02e9ceb988 1443417319 84c8d9b87b512f3fabe68675d6b12bec 1443417319 413a5978d14b93c1b640172214bee751 1443417319 15e1cf336625fec63e2a77d06b107e11...

These are not NCBI taxids, they are IDs that taxonkit creates automatically. So you don't have to worry about it, I think.

I usually run just 'mmseqs taxonomy'. Were you able to make it work?

Hi! I'm glad to see you are still working on it. I am still very interested! I just checked `metaeuk taxtocontig`, but I thought it used mmseqs2-like databases. Therefore, isn't...

I think I made it work? I used the source taxonomy file that you provided in the last comment and used taxonkit to generate the taxdump files. The taxonkit manual...

The taxonkit manual says that mmseqs2 databases require the taxondump to be ordered, and provides a script to do it, but it doesn't work as intended. This time, I built...

Hello! I've been testing lately doing contig taxonomic assignation with MMSEQS easy-taxonomy and VEBA microeuk v3 database (built as I mentioned in the last comments). I've been comparing it with...