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ABySS - Assembly By Short Sequences

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.



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

$ abyss-pe np=8

The command 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 commands are different, and the capitalization is significant.

Users may direct questions to