BWA-MEM is a fast, accurate algorithm for mapping DNA sequence reads to a reference genome, performing local alignment and producing alignment for different parts of the query sequence. It is the default algorithm in Burrows-Wheeler Aligner (BWA) for reads that are longer than 70bp and is designed for high-throughput sequencing technologies such as Illumina and Pacific Biosciences.

BWA-MEM can be deployed within Parabricks, a software suite designed for accelerated secondary analysis in genomics, bringing industry standard tools and workflows from CPU to GPU, and delivering the same results at up to 60x faster runtimes. FQ2BAM is the Parabricks wrapper for BWA-MEM, which will sort the output and can mark duplicates and recalibrate base quality scores in line with GATK best practices. A 30x whole genome can be run through FQ2BAM in as little as 7 minutes on an NVIDIA DGX system, compared to 4-9 hours on a CPU instance.

fq2bam performs the following steps:

• BWA-MEM alignment
• Co-ordinate sorting
• Mark duplicates
• BQSR

The user can decide to turn-off marking of duplicates. The BQSR step is only performed if the --knownSites input and --out-recal-file output options are provided.

Getting Started Quick Start Guide

For further information visit the fq2bam help page.

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