NVIDIA Clara™ Parabricks is a GPU-accelerated computational genomics application framework. It delivers high-throughput, high-accuracy DNA and RNA sequencing.
ANALYSIS
Accelerated Applications For Genomic Analysis
From FASTQ to Binary Alignment Map (BAM) to VCF, NVIDIA accelerates genomics analysis for somatic, germline and structural variant workflows, as well as improving sequencer speeds and consensus read base calling accuracy.
Clara Parabricks can be run on-premise or in the cloud
Robust HPC conducts training workshop that guides researchers on how to run their genomic analysis workloads with Clara Parabricks.
For R&D institutions that looking for a HPC cluster solution, Robust HPC provides the following:
USE CASES
How Clara Parabricks Is Making a Real-World Impact
Regeneron Genetics Center
See how Regeneron is using DeepVariant with Clara Parabricks to generate scalable, high-quality data that can be reproduced across the genomics community.
National Biobank of Thailand (NBT)
NBT reduced its whole genome sequencing data processing by four months and its individual user processing time from over 30 hours to just 1-2 hours with NVIDIA DGX A100 and Clara Parabricks.
Translational Genomics Research Institute (TGen)
With NVIDIA Clara Parabricks and NVIDIA V100 Tensor Core GPUs, TGen sped up genomic sequencing analysis by 6X to help determine personalized treatments for children with rare neurological disorders.
Washington University in Saint Louis (WUSTL)
Integrating GPU-based steps with NVIDIA Clara Parabricks enabled Tychele Turner of WUSTL to drastically reduce the runtime for de novo variant calling.
KEY FEATURES
The Parabricks Advantage
On a single server, the software can process more than 60 whole genomes per day
No need to sacrifice accuracy to reduce turnaround time. A suite of germline and somatic callers is available.
Create customized, accelerated pipelines by configuring over 33 tools for any specific pipeline or application need.
Reduce computing costs up to 50 percent by running 30–60X faster than CPU-only solutions.
SOFTWARE TOOLS OVERVIEW
The following standalone tools can be used with the NVIDIA Clara Parabricks Pipelines software. Please click on the tool names for tool specific options.
| Tool | Details |
| FQ2BAM | Align using bwa-mem, co-ordinate sort and mark duplicates, optionally you can run bqsr. |
| BQSR | Generate a BQSR report on a bam file. |
| APPLYBQSR | Apply a BQSR report on a bam file to generate new bam file. |
| HAPLOTYPECALLER | GPU-HaplotypeCaller for calling germline variants. |
| SAMTOOLS MPILEUP | Accelerated samtools mpileup to generate pileup from a bam file. |
| BCFTOOLS MPILEUP | Accelerated bcftools mpileup to generate pileup from a bam file. |
| BCFTOOLS CALL | Accelerated bcftools call variant caller. |
| SOMATICSNIPER | Accelerated Somaticsniper for tumor-normal analysis. |
| SOMATICSNIPER WORKFLOW | Somaticsniper workflow to generate VCF from BAM input files. |
| MANTA | Structural variant (SV) and indel caller from mapped paired-end sequencing reads. |
| STRELKA | SNP and indel caller from mapped paired-end sequencing reads. |
| STRELKA WORKFLOW | Strelka workflow to generate VCF from BAM/CRAM input files. |
| MUTECTCALLER | GPU-Mutect2 for tumor-normal analysis. |
| DEEPVARIANT | GPU-DeepVariant for calling germline variants. |
| CNVKIT | Accelerated copy number variant caller. |
| BAMMETRICS | Collect WGS Metrics on a bam file. |
| COLLECT MULTIPLE METRICS | Collect multiple classes of metrics for a bam file. |
| DBSNP | Annotate variants based on a variant database. |
| CNNSCOREVARIANTS | Filter variants using Convolutional Neural Network. |
| VQSR | Build a recalibration model to score variant quality and apply a score cutoff to filter variants. |
| TRIO COMBINE GVCF | Combine gVCF of 2 or 3 samples. |
| GLNEXUS | Scalable gVCF merging and joint variant calling for population sequencing projects. |
| INDEX GVCF | Index a VCF/gVCF file. |
| GENOTYPEGVCF | Convert a gVCF To VCF. |
| RNA FQ2BAM | Mapping RNA reads to a reference, using a two-pass mode to get better alignments around novel splice junctions. |
| STAR-FUSION | Uses the STAR aligner to identify candidate fusion transcripts. |
Resources
NVIDIA Clara Parabricks Datasheet
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