trimfq to drop seq under minlen and output cutpoints

lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats

MIT License

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trimfq to drop seq under minlen and output cutpoints #101

Open a1an77 opened 6 years ago

a1an77 commented 6 years ago

Hi, I needed to change the behaviour of the trimming function to drop reads shorter than minlen after trimming instead of providing low quality bases and I added an option to output the cut points (-1 if discarded) in a separate file. If you like the changes to be included I can open a pull request. Also added a Q option to set the threshold with a Phred score

tseemann commented 6 years ago

I think you can just seq trimfq ... | seqtk seq -L minlen ...

Might also be able to use seqtk seq -q PHRED .... to do the quality trimming.