dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
The Dazzler Scrubbing Suite produces a set of edited reads that are guaranteed
to (a) be continuous stretches of the underlying genome (i.e. no unremoved
adapters and not chimers) and (b) have no very low quality stretches (i.e. the
error rate never exceeds some reasonable maximum, 20% or so in the case of
Pacbio data). Its secondary goal is to do so with the minimum removal of data
and splitting of reads.
For a complete description of available commands and their options, see the
README file in /usr/share/doc/dascrubber/
daligner(1),
dazzdb(1).