Overview
Parabricks is a free software suite for performing secondary analysis of next generation sequencing (NGS) DNA and RNA data. It delivers results at blazing fast speeds and low cost. Parabricks can analyze 30x WGS (whole human genome) data in about 10 minutes, instead of 30 hours for other methods. Its output matches commonly used software, making it fairly simple to verify the accuracy of the output.
Under the hood, Parabricks achieves this performance through tight integration with GPUs, which excel at performing data-parallel computation much more effectively than traditional CPU-based solutions. Parabricks was built from the ground up by GPU computing and Deep Learning experts who wanted to develop the fastest and most efficient possible implementation of common genomics algorithms used in secondary analysis.
Parabricks delivers major improvements in throughput 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 user's requirements.
Learn more at the Parabricks developer page.
This table highlights a few benchmarks on two popular NVIDIA GPUs using 30x whole genome Illumina data.
NVIDIA H100 SXM GPU | NVIDIA L4 GPU Lowest cost/sample | |||
|---|---|---|---|---|
2 GPUs | 4 GPUs | 2 GPUs | 4 GPUs | |
|
Giraffe |
60.10 | 37.68 | 81.43 | 44.57 |
|
fq2bam (BWA-MEM) |
10.10 | 7.28 | 35.10 | 19.28 |
| DeepVariant | 7.60 | 5.90 | 13.83 | 8.03 |
| HaplotypeCaller | 8.63 | 4.17 | 14.2 | 7.03 |
These numbers were gathered by the NVIDIA Perflab team with internal nodes; please use them for reference only. Speeds can vary depending on the data set, GPU instance, host CPU, memory availability and other factors.
Parabricks is freely available as a public container on NGC for use on-premises or any cloud service platforms and providers. You can learn more about Parabricks on our webpage, including how to purchase enterprise support for Parabricks through NVIDIA AI Enterprise with guaranteed response times, priority security notifications and access to AI experts from NVIDIA. Users on DGX Cloud are able to utilize NVIDIA AI Enterprise for free.
See the following Cloud Startup guides for more information on using Parabricks in the cloud:
Parabricks supports the tools shown below:
Additionally, the Parabricks tool suite provides a number of variant calling pipelines that are each a combination of several individual tools, combining into one tool what would otherwise be a multi-step process. These pipelines are:
Parabricks has been tested on Dell, HPE, IBM, and NVIDIA servers at Amazon Web Services, Google Cloud, Oracle Cloud Infrastructure, and Microsoft Azure.