NAME

       nxtrim - <short_description>

SYNOPSIS

       nxtrim -1 R1.fastq.gz -2 R2.fastq.gz [options]

DESCRIPTION

       Program:        nxtrim Version:        v0.4.3 Contact:        joconnell@illumina.com

COPYRIGHT

       Copyright © 2016, Illumina, Inc. All rights reserved. See LICENSE for further details.

   Required arguments:
       -1 [ --r1 ] arg
              read 1 in fastq format (gzip allowed)

       -2 [ --r2 ] arg
              read 2 in fastq format (gzip allowed)

   Allowed options:
       -O [ --output-prefix ] arg
              output prefix

       --justmp
              just  creates  a  the mp/unknown libraries (reads with adapter at the start will be
              completely N masked)

       --stdout
              print trimmed reads to stdout (equivalent to justmp)

       --stdout-mp
              print only known MP reads to stdout (good for scaffolding)

       --stdout-un
              print only unknown reads to stdout

       --rf   leave mate pair reads in RF orientation [by default are flipped into FR]

       --preserve-mp
              preserve MPs even when the corresponding PE has longer reads

       --ignorePF
              ignore chastity/purity filters in read headers

       --separate
              output  paired  reads  in  separate   files   (prefix_R1/prefix_r2).   Default   is
              interleaved.

       -a, --aggressive
              more aggressive adapter search (see docs/adapter.md)

       -s, --similarity arg (=0.85)
              The  minimum  similarity between strings to be considered a match (Hamming distance
              divided by string length)

       -v, --minoverlap arg (=12)
              The minimum overlap to be considered for matching

       -l, --minlength arg
              (=21)      The minimum read length to output (smaller reads will be filtered)

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.