Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Open accessAbstract
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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Reads were mapped onto the final assembled transcripts using Bowtie to further assess and/or visualize the assembly.
“To further assess and/or visualize the assembly, we mapped the reads onto the final assembled transcripts using the Bowtie program [27] available at the Galaxy website (http://main.g2.bx.psu.edu/) [23]–[25].”
From Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.] (2012) · cites this paper as [27]
Mapping reads to specific genes is relatively straightforward with available bioinformatics tools, but using these tools to distinguish between reads derived from alternative alleles of the same gene remains challenging.
“Mapping reads to specific genes is relatively straightforward with the bioinformatics tools available today [10-13], but using these tools to distinguish between reads derived from alternative alleles of the same gene remains challenging [9].”
From Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome (2013) · cites this paper as [10]
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- Authors
- Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L.
- Affiliations
- University of Maryland, College Park (US)
- Corresponding author
- Langmead, Ben
- Venue
- Genome Biology
- Published
- 2009-03-04
- Volume
- 10
- Issue
- 3
- Pages
- R25-R25
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC2690996
- OpenAlex
- W2124985265
- Cited by
- 21,849
- References
- 29
- Citations by year
- 2026: 620 · 2025: 981 · 2024: 1140 · 2023: 1226 · 2022: 1405 · 2021: 1665 · 2020: 1652 · 2019: 1726 · 2018: 1653 · 2017: 1702 · 2016: 1538 · 2015: 1620 · 2014: 1565 · 2013: 1325 · 2012: 1029
- FWCI
- 267.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- University Libraries (University of Maryland) (submittedVersion)
- Digital Repository at the University of Maryland (University of Maryland College Park)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (R01HG004885)
- National Institute of General Medical Sciences (R01GM083873)
- U.S. National Library of Medicine (R01LM006845)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- Bowtie, human genome, memory-efficient alignment, parallel alignment, next-generation sequencing reads
- MeSH terms
- Algorithms, Base Sequence, Humans, Genome, Human, Sequence Alignment
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