Bowtie specifications


Unique identifier OMICS_00653
Name Bowtie
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ, FA
Output format SAM, FAI
Operating system Unix/Linux
Programming languages C, C++
License Artistic License version 2.0
Computer skills Advanced
Version 1.2.2
Stability Stable
Registration required No
Maintained Yes


  • bowtie-build
  • bowtie-inspect



Add your version



  • person_outline Ben Langmead <>

Bowtie articles

Bowtie citations

PMCID: 5954271

[…] reads from all libraries were filtered to discard low quality reads and trimmed to 75bp length using trimmomatic [60], then mapped onto the contigs or scaffolds of the considered species using bowtie2 [61]; for reads with multiple mappings, all of them were conserved. the scaffolding software besst [62, 63] was then used to detect potential scaffolding adjacencies between pairs of contigs […]

PMCID: 5943353

[…] dna-seq kit 6 s (rubicon genetics cat # r400523). libraries were sequenced on the illumina hiseq. 2500 dna sequencer platform on a single v2 rapid run flowcell. raw reads were aligned to hg38 using bowtie2. peaks enriched upon lincdusp pulldown vs. non-targeting control were called using macs software (version 1.4.0rc2) and filtered for peaks with greater than 5-fold enrichment […]

PMCID: 5933776

[…] 3 reagent kit. for comparison, draft genomes of usa100 (baa-1699) and usa300 (atcc-1556) reference strains were also generated in parallel., to identify snps between pairs of isolates, we used bowtie2 (v2.2.6) software [16] to map paired-end reads to the s. aureus reference sequence usa300_fpr3757 (atcc-1556) [17]. the usa300_fpr3757 contains three annotated plasmids (pusa01, pusa02, […]

PMCID: 5930841

[…] the rrna depletion efficiency., sequencing reads that passed standard illumina quality control procedures were used for the alignment and counting. transcriptome alignment was performed using bowtie version 0.12.7 [58], followed by probabilistic counting with rsem version 1.2.4 [59]. strand-specificity of the libraries (generated with dutp protocol) was accounted for as “–forward-prob 0” […]

PMCID: 5938390

[…] were performed by novogene bioinformatics technology co., ltd. (beijing, china) as previously described (liu b. et al., 2014). clean reads were mapped to the corresponding bacterial genomes using bowtie 2 software (langmead and salzberg, 2012). gene expression was calculated using the fpkm (expected number of fragments per kilobase of transcript sequence per millions of base pairs sequenced) […]

Bowtie institution(s)
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
Bowtie funding source(s)
Supported in part by US National Institutes of Health grants R01-HG006102 and R01-GM083873 and an Amazon Web Services in Education Research grant in July 2011.

Bowtie reviews

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clement GARCIA

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Great tools for read mapper

Arup Ghosh

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Bowtie is the most commonly used short read aligner after BWA. Tophat2 in tuxedo suite is based on bowtie.