abacas.rst

Abacas

Introduction ~~~~~~~~ Abacas is a tool for algorithm based automatic contiguation of assembled sequences.

For more information, please check its website: https://biocontainers.pro/tools/abacas and its home page: http://abacas.sourceforge.net.

Versions

• 1.3.1

Commands ~~~~~~~ - abacas.pl - abacas.1.3.1.pl

Module

You can load the modules by:

module load biocontainers
module load abacas

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 Abacas on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=abacas
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers abacas

abacas.pl -r cmm.fasta -q Cm.contigs.fasta -p nucmer -o out_prefix