ABySS
Description
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.
License
GNU GPL v3
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 abyss and load default version of abyss as
module avail abyss/ # list available modules module load abyss # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail abyss
and choose explicit version you want to use.
Parallel use
Newer AbySS versions use a different way how to use parallelization. Do not run mpirun -np 8 abyss-pe. To run ABySS with 8 threads (for example), use abyss-pe np=8. The abyss-pe driver script will start the MPI process, like so: mpirun -np 8 ABYSS-P. The example with ABySS 2.3.5 (prepared as Conda environment) is following:
module add conda-modules-py37 conda activate abyss_v2.3.5_py3.6 abyss-pe np=8 k=71 B=3G name=test_run ...
Version 2.1.5 was compiled with openmpi-3.1.2-gcc!
Documentation
https://github.com/bcgsc/abyss