ParDRe
Description
ParDRe is a parallel tool to remove duplicate reads. Duplicate reads can be seen as identical or nearly identical sequences with some mismatches. This tool will let the users to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset (e.g., assemblies, mappings, etc.).
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 pardre and load default version of pardre as
module avail pardre/ # list available modules module load pardre # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail pardre
and choose explicit version you want to use. Then run as
ParDRe -h
It can use MPI to parallelize calculations, e.g. on 8 CPU threads:
mpirun -n 8 ParDRe ...
Documentation
https://sourceforge.net/projects/pardre/ (PDF manual is part of package with source code)