genomicconsensus
Link to section 'Introduction' of 'genomicconsensus' Introduction
Genomicconsensus is the current PacBio consensus and variant calling suite.
For more information, please check its website: https://biocontainers.pro/tools/genomicconsensus.
Link to section 'Versions' of 'genomicconsensus' Versions
- 2.3.3
Link to section 'Commands' of 'genomicconsensus' Commands
- quiver
- arrow
- variantCaller
Link to section 'Module' of 'genomicconsensus' Module
You can load the modules by:
module load biocontainers
module load genomicconsensus
Link to section 'Example job' of 'genomicconsensus' Example job
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