Genomicconsensus

Introduction

Genomicconsensus is the current PacBio consensus and variant calling suite.

For more information, please check its website: https://biocontainers.pro/tools/genomicconsensus and its home page on Github.

Versions

2.3.3

Commands

quiver
arrow
variantCaller

Module

You can load the modules by:

module load biocontainers
module load genomicconsensus

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 Genomicconsensus on our clusters:

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

module --force purge
ml biocontainers genomicconsensus

quiver -j12 out.aligned_subreads.bam \
    -r All4mer.V2.01_Insert-changed.fa  \
    -o consensus.fasta -o consensus.fastq