nxtrim - <short_description>

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

nxtrim 0.4.3                                       April 2021                                          NXTRIM(1)

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

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

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

   Allowedoptions:-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)

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

       nxtrim - <short_description>

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