Genetically Improved BarraCUDA
W. B. Langdon, Brian Yee Hong Lam

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.
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