Abyss
Introduction
ABySS
is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.
Versions
2.3.2
2.3.4
Commands
ABYSS
ABYSS-P
AdjList
Consensus
DAssembler
DistanceEst
DistanceEst-ssq
KAligner
MergeContigs
MergePaths
Overlap
ParseAligns
PathConsensus
PathOverlap
PopBubbles
SimpleGraph
abyss-align
abyss-bloom
abyss-bloom-dbg
abyss-bowtie
abyss-bowtie2
abyss-bwa
abyss-bwamem
abyss-bwasw
abyss-db-txt
abyss-dida
abyss-fac
abyss-fatoagp
abyss-filtergraph
abyss-fixmate
abyss-fixmate-ssq
abyss-gapfill
abyss-gc
abyss-index
abyss-junction
abyss-kaligner
abyss-layout
abyss-longseqdist
abyss-map
abyss-map-ssq
abyss-mergepairs
abyss-overlap
abyss-paired-dbg
abyss-paired-dbg-mpi
abyss-pe
abyss-rresolver-short
abyss-samtoafg
abyss-scaffold
abyss-sealer
abyss-stack-size
abyss-tabtomd
abyss-todot
abyss-tofastq
konnector
logcounter
Module
You can load the modules by:
module load biocontainers
module load abyss
Example job
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run abyss on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=abyss
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers abyss
abyss-pe np=4 k=25 name=test B=1G \
in='test-data/reads1.fastq test-data/reads2.fastq'