Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Other free copies

• National Institutes of Health (ncbi.nlm.nih.gov)Preprint · Web page
• University of Maryland, College Park (doi.org)Free copy · Web page

Abstract

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu).