Genetically Improved BarraCUDA

TL;DR

This paper presents a genetically improved version of BarraCUDA, a GPU-accelerated DNA sequence aligner, achieving significant speed and accuracy enhancements over previous methods for next-generation sequencing data.

Contribution

The paper introduces a genetically optimized version of BarraCUDA that is up to three times faster and 60% more accurate than prior versions, leveraging GPU acceleration for DNA sequence alignment.

Findings

Up to three times faster than previous BarraCUDA versions.

60% more accurate on BioPlanet GCAT benchmark.

Aligns sequences up to ten times faster than BWA on a single GPU.

Abstract

BarraCUDA is a C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60percent more accurate on a short BioPlanet.com GCAT alignment benchmark. GPGPU Barracuda running on a single K80 Tesla GPU can align short paired end nextgen sequences up to ten times faster than bwa on a 12 core CPU.