fastqutils / trim

Removes linkers from 5' and 3' ends by performing local S/W alignments with
the linker sequences. This is best used when the sequencing is noisy with
a lot of low quality base calls. If there aren't expected to be many
mismatches or sequencing errors, use "fastqutils filter" as it uses a faster
sliding window method.

Usage: fastqutils trim {opts} filename.fastq{.gz}

You must specify at least one of the following:
  -5 seq      5' linker sequence to remove
  -3 seq      3' linker sequence to remove

  -len val         Minimum length of a read (discards shorter) [default: 25]
  -pct val         Required percent identity (0->1.0) [default: 0.8]
  -min val         Minumum number of bases to trim (or minumum dist. from the
                   ends) [default: 4]
  -failed fname    Write failed reads to file
  -v               Verbose output for each alignment