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

TitleUltrafast and memory-efficient alignment of short DNA sequences to the human genome
Publication TypeJournal Articles
Year of Publication2009
AuthorsLangmead B, Trapnell C, Pop M., Salzberg SL
JournalGenome BiologyGenome Biology
Volume10
Type of Article10.1186/gb-2009-10-3-r25
ISBN Number1465-6906
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.