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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
Copyright (c) 2011,2012,2013 Kevin Weitemier.
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
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.
fastq_collapse.py -i INFILE -o OUTFILE [-j JOB_ID]
Discards exact fastq sequence duplicates, preserving the highest average quality score. It also makes a file containing all the duplicated reads.