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lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats
MIT License
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Can seqtk filter the reads by length? #136

Open henganl2 opened 5 years ago

henganl2 commented 5 years ago

Hi,

I learned that seqtk can filter the minimum read length. For example, if I want the minimum read length to be 250 bp, the code will be: seqtk seq -L 250
Is this correct? since I can't find the -L function in the help page.

If this is correct, can I also set criteria for maximum read length?

Thanks!!

Best, Heng-An

tseemann commented 4 years ago

The -L option was not in older versions of seqtk. Type seqtk to see what version you are using:

Usage:   seqtk <command> <arguments>
Version: 1.3-r106

I don't think there is a max-len filter option.

You may want to look at seqkit seq which have

  -M, --max-len int               only print sequences shorter than the maximum length >
  -R, --max-qual float            only print sequences with average quality less than t>  -m, --min-len int               only print sequences longer than the minimum length (>

Please close this issue if this answers your questions. Thank you!