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Parabricks with Cudo Compute

Prerequisites

  • Create a project and add an SSH key
  • Optionally download CLI tool
  • Choose a VM with an NVIDIA GPU and Configure
  • Use the Ubuntu 22.04 + Nvidia drivers + Docker image (in CLI tool type -image ubuntu-nvidia-docker)

Running Parabricks with Docker

docker pull nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1

NGC tags can be found here More tutorials [here] (https://docs.nvidia.com/clara/parabricks/4.0.0/Tutorials.html)

Sample walkthrough

Download the sample data

wget -O parabricks_sample.tar.gz \
"https://s3.amazonaws.com/parabricks.sample/parabricks_sample.tar.gz"

Extract the data

tar xvf parabricks_sample.tar.gz

docker run \
      --gpus all \
      --rm \
      --volume $(pwd):/workdir \
      --volume $(pwd):/outputdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \
    pbrun fq2bam \
      --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
      --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz \
      --out-bam /outputdir/fq2bam_output.bam

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /workdir/parabricks_sample/Data/sample_1.fq.gz and
/workdir/parabricks_sample/Data/sample_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[PB Info 2022-Oct-14 09:54:15] ------------------------------------------------------------------------------
[PB Info 2022-Oct-14 09:54:15] ||                 Parabricks accelerated Genomics Pipeline                 ||
...

On a 4x Nvidia A4000 VM this process takes around 1m 30s

To view the results run:

apt install samtools
samtools view fq2bam_output.bam

HWI-D00127:570:HK3TJBCX2:2:2215:1035:92366	77	*	0	0	*	*	0	0	NAAAGACGGAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAGACGACCAATCTGACCAGCAAGGAAGCCAAGATGGGAAA	#<

For more help on Parabricks see the NVIDIA docs

Want to learn more?

You can learn more about using Parabricks on Cudo Compute by contacting us. Or you can just get started right away!