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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 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.

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