abyss
Link to section 'Introduction' of 'abyss' Introduction
ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.
For more information, please check its website: https://biocontainers.pro/tools/abyss and its home page on Github.
Link to section 'Versions' of 'abyss' Versions
- 2.3.2
- 2.3.4
- 2.3.8
Link to section 'Commands' of 'abyss' 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
Link to section 'Module' of 'abyss' Module
You can load the modules by:
module load biocontainers
module load abyss
Link to section 'Example job' of 'abyss' Example job
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'