Bowtie: Ultrafast and memory-efficient alignment of short reads to the human genome

[Ben Langmead]

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

http://genomebiology.com/2009/10/3/R25

Genome Biology 2009, 10:R25

Authors:

Ben Langmead , Cole Trapnell , Mihai Pop and Steven L Salzberg.
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA

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.

[ECO]

Congrats on the paper Ben. Nice work.

[araposo]

How does Bowtie align duplicate reads in default mode? Does it find a different alignment for each read or does it align all sequences in the same position?
I'm thinking specifically about repetitive regions of the genome and how Bowtie would deal with those.
Thank you,
Alexandre