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.

Resources

• ABySS documentation.

Hints

The command line to run multi-threaded on a single node with 16 cores would look like:

abyss-pe np=16

The command line to run the MPI version on 32 cores each for 1 hour would look like:

mpirun -hostfile=$PBS_NODEFILE -np=32 ABYSS-P

Note: the command names are different, and the capitalization is significant. These examples are just the application command lines, other elements of a batch job script must still be provided.

Users may direct questions to sys-help@loni.org.