Clara Parabricks
GCATemplates available: no
Clara Parabricks homepage
module spider parabricks
Clara Parabricks is a software suite that allows users to perform secondary analysis of next generation sequencing DNA and RNA data. The software incorporated into Clara Parabricks has been optimized to run on GPUs, drastically increasing the speed at which common NGS analyses and tasks can be completed.
Example 1: Complete germline analysis
#!/bin/bash
#SBATCH --job-name=parabricks-germline # set the job name to "parabricks-germline"
#SBATCH --time=02:00:00 # set the wall clock limit to 2 hours
#SBATCH --ntasks-per-node=1 # request one task per node
#SBATCH --cpus-per-task=48 # request 48 cpus per task
#SBATCH --mem=360G # request 360G of memory
#SBATCH --output=%x.%j.stdout # set standard output to write to <jobname>.<jobID>.stdout
#SBATCH --error=%x.%j.stderr # set standard error to write to <jobname>.<jobID>.stderr
#SBATCH --partition=gpu # request the gpu partition
#SBATCH --gres=gpu:h100:2 # request to h100 GPUs
# environment setup
module purge # ensure the working environment is clean
module load parabricks/4.5.0 # load the parabricks module
# run the parabricks germline command
pbrun germline --ref /path/to/indexed/genome.fasta \
--in-fq /path/to/forward_reads.fq /path/to/reverse_reads.fq \
--knownSites /path/to/known/variants.vcf.gz \
--out-bam output.bam \
--out-variants output.vcf \
--out-recal-file output.txt \
--num-gpus 2
#!/bin/bash
#SBATCH --job-name=parabricks-germline # set the job name to "parabricks-germline"
#SBATCH --time=02:00:00 # set the wall clock limit to 2 hours
#SBATCH --ntasks-per-node=1 # request one task per node
#SBATCH --cpus-per-task=64 # request 64 cpus per task
#SBATCH --mem=250G # request 250G of memory
#SBATCH --output=%x.%j.stdout # set standard output to write to <jobname>.<jobID>.stdout
#SBATCH --error=%x.%j.stderr # set standard error to write to <jobname>.<jobID>.stderr
#SBATCH --partition=gpu # request the gpu partition
#SBATCH --gres=gpu:a100:2 # request two A100 GPUs
# environment setup
module purge # ensure the working environment is clean
module load parabricks/4.0.1 # load the parabricks module
# run the parabricks germline command
pbrun germline --ref /path/to/indexed/genome.fasta \
--in-fq /path/to/forward_reads.fq /path/to/reverse_reads.fq \
--knownSites /path/to/known/variants.vcf.gz \
--out-bam output.bam \
--out-variants output.vcf \
--out-recal-file output.txt \
--num-gpus 2
#!/bin/bash
#SBATCH --job-name=parabricks-germline # set the job name to "parabricks-germline"
#SBATCH --time=02:00:00 # set the wall clock limit to 2 hours
#SBATCH --ntasks-per-node=1 # request one task per node
#SBATCH --cpus-per-task=96 # request 94 cpus per task
#SBATCH --mem=488G # request 488G of memory
#SBATCH --output=%x.%j.stdout # set standard output to write to <jobname>.<jobID>.stdout
#SBATCH --error=%x.%j.stderr # set standard error to write to <jobname>.<jobID>.stderr
#SBATCH --partition=gpu # request the gpu partition
#SBATCH --gres=gpu:a100:2 # request two A100 GPUs
# environment setup
module purge # ensure the working environment is clean
module load parabricks/4.1.1 # load the parabricks module
# run the parabricks germline command
pbrun germline --ref /path/to/indexed/genome.fasta \
--in-fq /path/to/forward_reads.fq /path/to/reverse_reads.fq \
--knownSites /path/to/known/variants.vcf.gz \
--out-bam output.bam \
--out-variants output.vcf \
--out-recal-file output.txt \
--num-gpus 2
Example 2: Aligning paired-end RNA-seq data to a genome
Index genomes before running the script with STAR 2.7.2b:
module spider STAR/2.7.2b
Then run the job script:
#!/bin/bash
#SBATCH --job-name=parabricks-rna # set the job name to "parabricks-rna"
#SBATCH --time=01:00:00 # set the wall clock limit to 1 hour
#SBATCH --ntasks-per-node=1 # request one task per node
#SBATCH --cpus-per-task=48 # request 48 cpus per task
#SBATCH --mem=360G # request 360G of memory
#SBATCH --output=%x.%j.stdout # set standard output to write to `<jobname>`.`<jobID>`.stdout
#SBATCH --error=%x.%j.stderr # set standard error to write to `<jobname>`.`<jobID>`.stderr
#SBATCH --partition=gpu # request the gpu partition
#SBATCH --gres=gpu:h100:2 # request two h100 GPUs
# environment setup
module purge # ensure the working environment is clean
module load parabricks/4.5.0 # load the parabricks module
pbrun rna_fq2bam \
--ref /path/to/indexed/genome.fasta \
--genome-lib-dir /path/to/indexed/genome/directory \
--output-dir ./
--in-fq /path/to/forward_reads.fq /path/to/reverse_reads.fq \
--out-bam output.bam \
--num-gpus 2 \
--out-prefix
#!/bin/bash
#SBATCH --job-name=parabricks-rna # set the job name to "parabricks-rna"
#SBATCH --time=01:00:00 # set the wall clock limit to 1 hour
#SBATCH --ntasks-per-node=1 # request one task per node
#SBATCH --cpus-per-task=64 # request 64 cpus per task
#SBATCH --mem=250G # request 250G of memory
#SBATCH --output=%x.%j.stdout # set standard output to write to `<jobname>`.`<jobID>`.stdout
#SBATCH --error=%x.%j.stderr # set standard error to write to `<jobname>`.`<jobID>`.stderr
#SBATCH --partition=gpu # request the gpu partition
#SBATCH --gres=gpu:a100:2 # request two T4 GPUs
# environment setup
module purge # ensure the working environment is clean
module load parabricks/4.0.0 # load the parabricks module
pbrun rna_fq2bam \
--ref /path/to/indexed/genome.fasta \
--genome-lib-dir /path/to/indexed/genome/directory \
--output-dir ./
--in-fq /path/to/forward_reads.fq /path/to/reverse_reads.fq \
--out-bam output.bam \
--num-gpus 2 \
--out-prefix
#!/bin/bash
#SBATCH --job-name=parabricks-rna # set the job name to "parabricks-rna"
#SBATCH --time=01:00:00 # set the wall clock limit to 1 hour
#SBATCH --ntasks-per-node=1 # request one task per node
#SBATCH --cpus-per-task=48 # request 96 cpus per task
#SBATCH --mem=488G # request 488G of memory
#SBATCH --output=%x.%j.stdout # set standard output to write to `<jobname>`.`<jobID>`.stdout
#SBATCH --error=%x.%j.stderr # set standard error to write to `<jobname>`.`<jobID>`.stderr
#SBATCH --partition=gpu # request the gpu partition
#SBATCH --gres=gpu:a100:2 # request two A100 GPUs
# environment setup
module purge # ensure the working environment is clean
module load parabricks/4.0.1 # load the parabricks module
pbrun rna_fq2bam \
--ref /path/to/indexed/genome.fasta \
--genome-lib-dir /path/to/indexed/genome/directory \
--output-dir ./
--in-fq /path/to/forward_reads.fq /path/to/reverse_reads.fq \
--out-bam output.bam \
--num-gpus 2 \
--out-prefix