Clara Parabricks is a software suite for delivering genomic analysis on GPU at blazing fast speeds and low cost, including secondary analysis of next generation sequencing (NGS) DNA and RNA data. Parabricks can analyze 30x whole genome sequencing (WGS) data in as little as 25 minutes on a single GPU server, instead of 30 hours in a CPU-based environment. Its output also matches commonly used software, making it fairly simple to verify the accuracy of the output. In this Lab, we will walk you through how to use three of our most used tools.
The fq2bam tool aligns, sorts (by coordinate), and marks duplicates in pair-ended FASTQ file data
Haplotypecaller for gold-standard GATK best practices variant calling
DeepVariant for high-accuracy deep learning based variant calling
The data files used in these examples are a 30X short-read human data generated from a child in a trio sequenced by the Genome In A Bottle Consortium.