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Masking or deduplication tool

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

deduplication masking fasta
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updated by GenoMax GenoMax • written by Raygozak Raygozak

1 answer

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/

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written by GenoMax GenoMax

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