Simple utilities operating on FASTQ files
Homed at: https://github.com/zwets/fastq-utils
I wrote these tiny tools whenever searching for them seemed to take longer than just write them. You may find comparable functionality in for instance NGSTools.
| Tool | Function |
|---|---|
fastq-mask |
Convert bases not passing quality threshold to lowercase or N |
fastq-rc |
Reverse complement a FASTQ file |
fastq-stats |
Compute number of reads, bases, and bases passing a Phred threshold in a FASTQ file |
fastq-unbreak |
Revert multi-line FASTQ (such as emitted by vcfutils.pl vcf2fq) to standard FASTQ |
fastq-to-fasta |
Convert FASTQ to FASTA |
fasta-to-fastq |
Convert FASTA to FASTQ |
All tools read from standard input and write to standard output. Just pipe them together. For instance,
... | vcfutils.pl vcf2fq | fastq-unbreak | fastq-mask -r | fastq-to-fasta
When the input is compressed, zcat is your friend:
zcat myfile.fq.gz | fastq-stats
All tools are plain vanilla C++. To compile, run make.
fastq-utils - simple utilities operating on fastq files Copyright (C) 2020 Marco van Zwetselaar io@zwets.it
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/.