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Structural variants can be pathogenic for diseases, such as Lou Gehrig’s disease (ALS), Parkinson’s disease, and cardiac diseases. This has resulted in a multitude of improvements for the sequencing community, including a greater understanding of structural variants (large insertions, deletions, inversions, duplications, and so on). Lower levels of ambiguity and alignment error make long-read sequencing better for more challenging parts of the genome (for example, highly repetitive regions) or for assembling a genome de novo (without a provided reference). Most prominently, the reads are more easily assembled into the full genome. Long-read sequencing, the capability of sequencing significantly longer fragments of DNA, has multiple inherent advantages over traditional short-read sequencing. Parabricks v4.1 optimization of the PacBio model for DeepVariant Supporting long-read analysis Sign up for notification of the Parabricks 4.1 release, or try the prerelease DeepVariant re-training tool.įigure 1. Compatibility with the new NVIDIA H100 GPU, which includes a powerful DPX instruction for boosting dynamic programming algorithms like Smith-Waterman for local sequence alignment.

Further acceleration of the short-read germline pipeline for a 30x whole genome in 16 mins on a DGX A100 GPU compared to 21 mins in v4.0 and ~24 hours on CPU-only.New accelerated DeepVariant variant caller for PacBio data with an 8-minute runtime for a 30x whole genome on 2xA100 GPUs.New accelerated Minimap2 tool for alignment of PacBio’s long reads.

An end-to-end (FastQ-to-VCF) accelerated workflow for PacBio, which will be made available on the Parabricks workflows on GitHub, Terra.Bio, and other cloud platforms.

A new DeepVariant Re-Training tool, to enable anyone to re-train or fine-tune DeepVariant for their own data, enabling more accurate variant calling (available now on NGC).

A 30x whole genome can now be analyzed in just 16 minutes compared to ~24 hours on CPU, translating to the analysis of up to 30,000 whole genomes a year on a single server. It contains a variety of optimized and AI-based industry-standard genomic tools delivering up to 80x acceleration over CPU-based tools and reducing compute costs by up to 50%.

NVIDIA Parabricks is free to use with an option for paid enterprise support. The release includes a new workflow for PacBio long-read data, featuring an accelerated Minimap2 tool and Google’s DeepVariant for full GPU-enabled, end-to-end analysis of PacBio data. The upcoming 4.1 release of NVIDIA Parabricks, a suite of accelerated genomic analysis applications, goes further than ever before in accelerating sequencing alignment and increasing the accuracy of deep learning variant calling.