- 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.
- ABySS homepage
- Our current installation has the maximum k-mer length
"maxk"set to 76.
- Here is an example of a submission script:
#$ -cwd #$ -l h_rt=01:00:00 #$ -pe openmp 4 module purge module load gcc openmpi/gcc abyss abyss-pe k=25 name=test se=test_reads.fa
- Known problems
- There are problems with some test jobs spanning multiple hosts, so we currently advise using the