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.

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'