fq_interleave - interleave paired FASTQ files
This documentation refers to v0.202
fq_interleave [--check --rename] reads1 reads2 > interleaved_reads
A simple script to interleave two paired FASTQ files (alternate forward/reverse reads in a single output file). This requires that the two files correspond exactly in terms of number and order of the paired reads ('--check' will make sure of this and throw an error otherwise). Interleaved FASTQ is sent to STDOUT.
Name of input file for forward reads (required)
Name of input file for reverse reads (required)
Check each pair of input reads to make sure names match (slower but more rigorous)
Renames forward and reverse reads to follow the ".../1" and .../2" naming convention (required for some programs). Everything at and after the first whitespace or end-of-line is replaced with the corresponding tag above.
Name of output file to write to (instead of the default STDOUT)
Force overwrite of output file even if it exists
As yet undiscovered. Please reports bugs to the GitHub repository issue tracker.
Jeremy Volkening (jeremy.volkening@base2bio.com)
Copyright 2014-2023 Jeremy Volkening
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.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.