Compiling ABySS
ABySS is Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler[1]
Download♯
Download the source package from the official website: http://www.bcgsc.ca/platform/bioinfo/software/abyss
Dependencies♯
Requires:
- sparsehash[2]
Compiling with GCC♯
t.b.a.
Usage♯
Please consult ABySS documentation.
Multi-threaded and MPI♯
Multi-threaded processes run on a single node. MPI jobs run on multiple nodes.
To run multi-threaded ABySS, your job must request a shm "parallel environment" (PE) with the appropriate number of threads to be run. To run an MPI version, request openmpi_ib, openmpi_ib_rr, or openmpi_rankfile PE.
See the article on Writing Job Scripts.