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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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“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]
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“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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Metadata
- 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 › Mathematics › Theoretical Computer Science › 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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