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:
BioContainers: https://biocontainers.pro/tools/abyss
Home page: https://github.com/bcgsc/abyss/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.3.2, 2.3.4, 2.3.8

BELL

2.3.2, 2.3.4, 2.3.8

GAUTSCHI

2.3.2, 2.3.4, 2.3.8

NEGISHI

2.3.2, 2.3.4, 2.3.8

SCHOLAR

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 clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers abyss

# Your abyss workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers abyss

# Your abyss workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers abyss

# Your abyss workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers abyss

# Your abyss workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers abyss

# Your abyss workflow...