Hi,
can anybody suggest a tool which aligns a targeted sequence (10 kb) against contigs/scaffolds or long reads, then removes that sequence from the contig and if necessary splits the contig into two if the undesired sequence is flanked by other sequence?
I could script this with BLAST or BWAmem coordinate alignments but I'd rather not reinvent the wheel if there is a tool which does this already. Most contaminant (adapter) trimming tools are designed for short stretches of sequence.
Thanks
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written
by
mz1101 •
1 answer
You might try BBMap's BBMask, which can mask a sequence using a sam file, converting all covered bases bases to N or lowercase. It can additionally split the result into contiguous sequences of unmasked bases only and discard the masked regions, which sounds like what you are looking for.
bbmask.sh in=sequence.fa sam=mapped.sam masklowentropy=f split=t out=split.fa
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