parabricks

Link to section 'Description' of 'parabricks' Description

NVIDIAs Clara Parabricks brings next generation sequencing to GPUs, accelerating an array of gold-standard tooling such as BWA-MEM, GATK4, Googles DeepVariant, and many more. Users can achieve a 30-60x acceleration and 99.99% accuracy for variant calling when comparing against CPU-only BWA-GATK4 pipelines, meaning a single server can process up to 60 whole genomes per day. These tools can be easily integrated into current pipelines with drop-in replacement commands to quickly bring speed and data-center scale to a range of applications including germline, somatic and RNA workflows.

Link to section 'Versions' of 'parabricks' Versions

Scholar: 4.0.0-1
Gilbreth: 4.0.0-1
Anvil: 4.0.0-1

Link to section 'Module' of 'parabricks' Module

You can load the modules by:

module load ngc
module load parabricks

Link to section 'Example job' of 'parabricks' 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 parabricks on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 8
#SBATCH --gpus-per-node=1
#SBATCH --job-name=parabricks
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc parabricks