Which is faster: Bowtie2GP > Bowtie > Bowtie2 > BWA

TL;DR

This paper presents a genetically programmed version of Bowtie2 that significantly outperforms BWA in speed and memory efficiency while maintaining similar accuracy in DNA read alignment.

Contribution

The authors used genetic programming to automatically enhance Bowtie2, resulting in a faster, more memory-efficient DNA alignment tool with comparable accuracy to existing methods.

Findings

Bowtie2GP is over four times faster than BWA.

Bowtie2GP uses less memory than BWA.

Bowtie2GP maintains similar accuracy in human genome alignment.

Abstract

We have recently used genetic programming to automatically generate an improved version of Langmead's DNA read alignment tool Bowtie2 Sect.5.3 RN/12/09. We find it runs more than four times faster than the Bioinformatics sequencing tool (BWA) currently used with short next generation paired end DNA sequences by the Cancer Institute, takes less memory and yet finds similar matches in the human genome.