NVIDIA Parabricks Amazon Linux

What is NVIDIA Parabricks?

NVIDIA Parabricks is an accelerated compute framework that supports applications across the genomics industry, primarily supporting analytical workflows for DNA, RNA, and somatic mutation detection applications. With industry leading compute times, Parabricks rapidly converts a FASTQ file to a VCF using multiple, industry validated variant callers and also includes the ability to QC those variants. As Parabricks is based upon publicly available tools, results are easy to verify and combine with other publicly available datasets.

More information is available on the Parabricks Product Page. Detailed installation, usage, and tuning information is available in the Parabricks user guide.

Answers to common questions can be found on the Parabricks developer forum.

The Parabricks Amazon Linux docker image can be obtained by running the following command:

$ docker pull nvcr.io/nvidia/clara/nvidia_clara_parabricks_amazon_linux:<TAG>

An example run of the fq2bam tool using the container will be as follow:

#This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.
$ docker run --rm --gpus all -v <INPUT_DIR>:/workdir \
-v <OUTPUT_DIR>:/outputdir \
-v <TMP_DIR>:/raid/myrun -w /workdir \
nvcr.io/nvidia/clara/clara-parabricks:<TAG> \
pbrun fq2bam \
--ref /workdir/${REFERENCE_FILE} \
--in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2}  \
--knownSites /workdir/${KNOWN_SITES_FILE} \
--out-bam /outputdir/${OUTPUT_BAM} \
--out-recal-file /outputdir/${OUTPUT_RECAL_FILE}

License An End User License Agreement is included with this product. By pulling and using the Parabricks container you accept the terms and conditions of this license.

How is this Amazon Linux container meant to be used?

The Parabricks container normally uses Ubuntu as the base image for the Docker environment. This is incompatible with many AWS services. As a result, this new container is based on Amazon Linux instead of Ubuntu. Everything else in the container works the same, however, now there is native support for services such as Amazon Batch and Amazon Health Omics which require Amazon Linux for their Docker containers.

An example workflow that uses this container is the Amazon Omics Private Workflows for Parabricks