NVIDIA CLARA PARABRICKS DOCUMENTATION

What is CLARA PARABRICKS Pipelines?

Parabricks is a software suite for performing secondary analysis of next generation sequencing (NGS) DNA and RNA data. A major benefit of Parabricks is that it is designed to deliver results at blazing fast speeds and low cost. Parabricks can analyze whole human genomes in about 45 minutes, compared to about 30 hours for 30x WGS data. The best part is the output results exactly match the commonly used software. So, it’s fairly simple to verify the accuracy of the output.

Why use CLARA PARABRICKS Pipelines?

Under the hood, it 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.

You can learn more at https://developer.nvidia.com/clara-parabricks

SOFTWARE OVERVIEW

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 data pipeline which takes raw data and transforms it according to the user’s requirements.

The Parabricks software supports the Tools shown below:

It supports the Pipelines shown below:

The Parabricks software can be configured to run specific accelerated tools or run full pipelines that are commonly used. The standalone tools page covers individual tools and the pipelines page discuses how to run commonly used pipelines.

NVIDIA Parabricks’ pipelines have been tested on Dell, HPE, IBM, and NVIDIA servers at Amazon Web Services, Google Cloud, Oracle Cloud Infrastructure, and Microsoft Azure.

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.

Compatible CPU Software Versions

Here are the versions that you can find in this package

Tool	Version
bwa	0.7.15
GATK	4.1.0.0
STAR	2.7.2a
STAR-Fusion	1.7.0
Deepvariant	1.0.0
lofreq	2.1.5
somaticsniper	1.0.5.0
cnvkit	0.9.7
glnexus	1.2.7
strelka	2.9.0
manta	1.6.0
samtools	1.10
bcftools	1.10.2

Pipelines Overview

The following standalone pipelines can be used with the NVIDIA Clara Parabricks Pipelines software. Please click on the tool names for tool specific options.

Pipeline	Functionality
GERMLINE PIPELINE	Detect germline variants for a given sample from fastq files. Compatible with GATK4 best practices.
DEEPVARIANT GERMLINE PIPELINE	Detect germline variants for a given sample from fastq files using DeepVariant caller.
HUMAN_PAR PIPELINE	Detect germline variants for a given sample from fastq files with correct ploidy values for human sex chromosome handling. Compatible with GATK4 best practices.
SOMATIC PIPELINE	Detect somatic variants for a given tumor/normal fastq files. Compatible with GATK4 best practices.
RNA PIPELINE	Detect RNAseq short variants (SNPs + Indels). Compatible with GATK4 best practices.
Denovo PIPELINE	(BETA) De novo mutation pipeline with 3 samples for de novo variant detection