NVIDIA Parabricks is a software suite for genomic analysis. It delivers major improvements in throughput time for common analytical tasks in genomics, including germline and somatic analysis. The core of the Parabricks software is its tight integration with the GPU, which takes raw data and transforms it according to the users requirements.
Parabricks has been tested on Dell, HPE, IBM, and NVIDIA servers at Amazon Web Services, Google Cloud, Oracle Cloud Infrastructure, and Microsoft Azure.
Parabricks supports the tools shown below:
The somatic (Somatic Variant Caller), germline (GATK Germline Pipeline), pacbio_germline (Beta), and deepvariant_germline tools are actually a collection of several individual tools that are frequently run together, each grouped as a single command for the users convenience. For example, deepvariant_germline takes FASTA and FASTQ files as input and produces a VCF and BAM file as output. Internally, it runs BWA mem alignment, performs coordinate sorting, marks duplicates, and then runs DeepVariant.
The Tool Reference page lists all the individual tools. The Parabricks WDL/Nextflow Workflows page discusses the use of Parabricks with WDL and Nextflow. The Compatible CPU Software Versions page lists the open-source CPU tools Parabricks is compatible with.