Ultrafast and Memory-efficient Alignment of Short DNA Sequences to the Human Genome

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2009 Mar 6

PMID 19261174

Citations 12547

Authors

Ben Langmead

Cole Trapnell

Mihai Pop

Steven L Salzberg

Affiliations

Soon will be listed here.

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).

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