Fastq Pair
Description
Rewrite paired end fastq files to make sure that all reads have a mate and to separate out singletons.
License
MIT License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of fastq-pair and load default version of fastq-pair as
module avail fastq-pair/ # list available modules module load fastq-pair # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail fastq-pair
and choose explicit version you want to use.
fastq_pair [options] [fastq file 1] [fastq file 2]
Documentation
https://github.com/linsalrob/fastq-pair#running-fastq_pair