ABySS
Revision as of 14:35, 6 September 2018 by Moskalenko (talk | contribs)
Description
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
Environment Modules
Run module spider abyss to find out what environment modules are available for this application.
Serial
- abyss
Parallel (MPI)
- intel/2016.0.109
- openmpi/1.10.2
- abyss/1.9.0
System Variables
- HPC_{{#uppercase:abyss}}_DIR - installation directory
How To Run
The abyss-pe is hardcoded to use mpiexec, so you need to set the following variable in your abyss job script before calling abyss-pe to explicitly allow mpiexec usage, which is disabled by default:
export HPC_USE_MPIEXEC=1