Unclassified vs "not classified" about cat HOT 3 CLOSED

This makes sense. Thank you so much for your quick reply.

Kathie

from cat.

Hi,
I also had some contigs like this. If you look at the taxonomic lineage (numeric), you should see, that those are classified as 131567 or even the root (1). This can be caused by classifications as environmental samples.
Just to check this is the case, would you mind sharing the affected contigs or the CAT output?
Have a nice day,
Lukas Jansen

from cat.

Hi @mihinduk and @Finesim97,

Yes you are right! Sometimes a contig is classified at a higher level than superkingdom, in which case CAT considers it classified but you won't find any classification on the official ranks.

The logic for this behaviour is that giving names to the lineage at official ranks is a post-classification step, and CAT is agnostic as to which level you want a classification to be made before something is called unclassified.

Hope this helps!

Best wishes,

Bastiaan

from cat.