For unbinned contigs, run CAT in "contig mode" (CAT_pack contigs) instead of "bin mode" (CAT_pack bins)

[amizeranschi]

Hi !
I've been testing CAT for taxonomic classification of bins, which were created with metabat2 + maxbin2 and refined with das tool. I noticed that the pipeline runs CAT both on the bins and on the unbinned contigs. However, the latter are treated as one huge bin, and thus a single taxonomic label gets assigned to the whole lot:

For example:

MEGAHIT-DASToolUnbinned-PC2.fa	taxid assigned	based on 261612/286893 ORFs	1;131567;2	1.00;1.00;0.98	root (no rank): 1.00	cellular organisms (no rank): 1.00	Bacteria (superkingdom): 0.98

and:

MEGAHIT-DASToolUnbinned-PM2.fa	taxid assigned	based on 453818/502870 ORFs	1;131567;2;1224	1.00;1.00;0.97;0.35	root (no rank): 1.00	cellular organisms (no rank): 1.00	Bacteria (superkingdom): 0.97	Proteobacteria (phylum): 0.35

In both cases, there are plenty of ORFs that could be viral or eukaryotic and it would be interesting to have the ability to zoom in and see what is actually in there at a contig level.

For the unbinned contigs, it would make more sense to run CAT in "contig mode" (CAT_pack contigs) instead of "bin mode" (CAT_pack bins).
See: https://github.com/MGXlab/CAT_pack?tab=readme-ov-file#running-catbatrat

[amizeranschi]

Relevant thread on #Slack: https://nfcore.slack.com/archives/CE9MS66BS/p1734430094593639