How to get the unclassified sequences (sqm_longreads)

[inej90]

Dear Javier and Fernando,

I've ran one sample (milk) using sqm_longreads. I got ~45% of unclassified. I want now to extract theses sequences to do a Blast to see to which organisms they correspond. From which file of outputs can I get the information?

Thank you in advance.

[fpusan]

There is no direct way of doing it but it can be done.
The *.out.allreads file has all the reads that got either a taxonomic or functional annotation.
So you will need to select all the reads that are NOT in that file, and also those that are in that file but have no taxonomic annotation.