Abyss

Introduction

ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.

Versions

• 2.3.7

Commands

• ABYSS

• 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-P

• 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

• AdjList

• Consensus

• DAssembler

• DistanceEst

• DistanceEst-ssq

• KAligner

• konnector

• logcounter

• MergeContigs

• MergePaths

• Overlap

• ParseAligns

• PathConsensus

• PathOverlap

• PopBubbles

• SimpleGraph

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=abyss       # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load abyss/XXXX ### Latest version is recommended.