GitHub - listonlab/fastq_collapse: Discards exact fastq sequence duplicates, preserving the highest average quality score. It also makes a file containing all the duplicated reads.

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Discards exact fastq sequence duplicates, preserving the highest average quality score. It also makes a file containing all the duplicated reads.

GPL-3.0 license

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fastq_collapse.py - Discards exact fastq sequence duplicates, preserving the
    highest average quality score. It also makes a file containing all the 
    duplicated reads.

                                      by
                                Kevin Weitemier
                                 February 2013

Copyright (c) 2011,2012,2013  Kevin Weitemier.

Version 0.03

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version. A copy of this license is distributed with the program and available
at <http://www.gnu.org/licenses/>.
Great effort has been taken to make this software perform its said
task, however, this software comes with ABSOLUTELY NO WARRANTY,
not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Input - A fastq file where each sequence occupies four (4) lines.

Usage:

fastq_collapse.py -i INFILE -o OUTFILE [-j JOB_ID]