Understanding Genetic Diversity from Pangenomes
NVIDIA Parabricks v4.4 introduces new features and functionality, including accelerated pangenome graph alignment with Giraffe. The core new feature is single-end and paired-end support for Giraffe, as well as additional functionality for Minimap2 and GATK HaplotypeCaller, and tool performance improvements.
New Features
- GPU-accelerated Giraffe with single-end and paired-end support
- Pbmm2 wrapper for native PacBio input and output of Minimap2
- Allele option support in GATK HaplotypeCaller
- Support for unaligned BAMs: FQ2BAM (BWA-MEM) and Minimap2
Improved Features
- Faster Minimap2 for PacBio and Oxford Nanopore (ONT) data
- DeepVariant acceleration for ONT data
- Faster CRAM file writer (2x acceleration over CPU-only)
- 30-minute end-to-end 30x whole genome sequencing (WGS) germline on a single-GPU system (NVIDIA Grace Hopper)
New Collaborations and Benchmarks
- Complete Genomics data supported on Parabricks
- Parabricks now available on Basepair platform
- Updated benchmarks, including DeepSomatic and Giraffe
Accelerating Pangenome Alignment with Giraffe
Giraffe is a software tool to support pangenome graph alignment. Built by the University of California, Santa Cruz (UCSC), it is used particularly in the context of large-scale genomic sequencing projects and helps with alignment, assembly, and variant calling. Giraffe enables new genomic sequences to be compared to a pangenome—not just a single reference genome.
Graph Genomes
To represent pangenome data, graph genomes provide a unified framework for representing the genetic variation of multiple genomes. The graph structure of the data provides easier understanding of structural changes, including insertions, deletions, and rearrangements.
Basepair
Basepair is a next-generation sequencing (NGS) data analysis platform. Their point-and-click user interface helps make genomic data analysis and visualization more accessible to a broader range of scientists. Now, users can supercharge their genomic data analysis by using Parabricks on Basepair, powered by HealthOmics from AWS.
Latest Parabricks Benchmarks
In addition to new features and upgrades for each release, NVIDIA continuously works to improve benchmark performance across instruments, tools, and GPUs. Table 1 outlines the latest benchmarks on the most popular NVIDIA GPUs for the fastest speed (NVIDIA H100) and lowest cost per sample (NVIDIA L4)–including Giraffe from Parabricks v4.4 and DeepSomatic from v4.3.1.
Get Started
With the NVIDIA Parabricks v4.4 release, scientists and researchers using graph genomes can now access Giraffe for pangenome alignment. Parabricks v4.4 supports the groundbreaking tool from UCSC by powering an accelerated version of Giraffe to help discover new biological insights—now even faster.
Conclusion
The NVIDIA Parabricks v4.4 release enables scientists and researchers to use Giraffe for pangenome alignment, accelerating the process of understanding genetic diversity. By leveraging the power of graph genomes and GPU-accelerated computing, researchers can uncover new biological insights and make significant contributions to the field of genomics.
Frequently Asked Questions
Q: What is pangenome alignment?
A: Pangenome alignment is a method of comparing new genomic sequences to a pangenome, rather than a single reference genome.
Q: What is Giraffe?
A: Giraffe is a software tool for supporting pangenome graph alignment, built by the University of California, Santa Cruz (UCSC).
Q: What is Parabricks?
A: Parabricks is a scalable genomics analysis software suite that solves omics challenges with accelerated computing and deep learning to unlock new scientific breakthroughs.
Q: What is the main benefit of using Parabricks v4.4?
A: The main benefit of using Parabricks v4.4 is the accelerated pangenome graph alignment with Giraffe, enabling researchers to uncover new biological insights even faster.
