ABySS

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Description
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.
Modulefile
abyss
Documentation
ABySS homepage
The current ACEnet installation has the maximum k-mer length "maxk" set to 76.
Usage
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 openmp parallel environment.
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