Journal
GENOME BIOLOGY
Volume 10, Issue 3, Pages -Publisher
BMC
DOI: 10.1186/gb-2009-10-3-r25
Keywords
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Funding
- NIH [R01-LM006845, R01-GM083873]
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [R01HG004885] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM083873] Funding Source: NIH RePORTER
- NATIONAL LIBRARY OF MEDICINE [R01LM006845] Funding Source: NIH RePORTER
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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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