Masking or deduplication tool

Question

[Raygozak]

Hi I was wondering if there is a tool, that given a refernce fasta file "A" and a query file "B" (also fasta), it would output trimmed sequences according to file "A". That I would be left with sequences or subsequences from "B" that are not contained in file "A"?

Thanks

Answer 1

[GenoMax]

You can try any scan/trim program for this. I recommend bbduk.sh from BBMap suite. You may need to trim left and right and be creative.

A guide is available for bbduk.sh: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/