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 docker image can be obtained by running the following command:

$ docker pull nvcr.io/nvidia/clara/clara-parabricks:<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}

NOTE: These instructions and commands are valid for Parabricks versions 4.0.1-1 and above only. For earlier versions, please visit Parabricks user guides for each specific older version. You will need an installer for versions prior to v4.0.1-1. Instructions for this are also in the Parabricks user guides.

License

By pulling and using the Parabricks container, you accept the terms and conditions of the NVIDIA AI Product Agreement. For enterprise support, register for a free evaluation license to try NVIDIA AI Enterprise on your compatible, on-premises system or on the cloud.