ABySS

module avail abyss/

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.

Usage

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 an environment) is following:

module add mambaforge
mamba 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!