Bowtie2 protocols

Bowtie2 specifications


Unique identifier OMICS_31633
Name Bowtie2
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, C++
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Benjamin Langmead <>

Additional information

Publication for Bowtie2

Bowtie2 IN pipelines

PMCID: 5743717
PMID: 29290775
DOI: 10.7150/jca.21925

[…] the human genome hg19 using tophat. unmapped reads were filtered out. transcripts were assembled by cufflink. differential expression of transcripts was estimated by cuffdiff 9. for chip-seq data, bowtie2 was used for mapping the chip-seq data to the human genome hg19. data from repeated experiments were merged for analysis. unmapped reads were filtered out. high-confidence peaks were called […]

PMCID: 5752202
PMID: 29297465
DOI: 10.7554/eLife.31216.024

[…] for further analysis and were allocated into two files according to snp mapping. each file was then converted back into fastq format using seqtk 1.0 ( and remapped with bowtie2 to the genome corresponding with its snp alignment. to adjust for the variable mapping efficiency of each snp-parsed file to either mauriceville or oakridge, samples were normalized using […]

PMCID: 5753479
PMID: 29298680
DOI: 10.1186/s12864-017-4382-2

[…] p. formosa and the three sexual species (p. latipinna, p. mexicana, and p. reticulata)., processed reads of each species were mapped back to the combined transcripts of all three species with bowtie2 using strict mapping parameters (no-discordant | no-mixed | score-min l,-0.1,-0.1). then, the transcripts were clustered with corest (v1.06) [58] and for each gene cluster, the number […]

PMCID: 5754085
PMID: 29300744
DOI: 10.1371/journal.pone.0189185

[…] empty reads, low-quality sequences, and short reads. the high-quality reads were aligned to the phaseolus vulgaris genome (v1.0), available in phytozome (joint genome institute), using tophat2/bowtie2 [21, 22]. reads overlapping with the annotation range of interest were counted for each sample using the “summarizeoverlaps” function [23]. read counting was performed for exonic gene regions […]

PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] were mapped randomly., abundance of transcripts were determined by mapping quality-filtered and adapter-trimmed reads (trimmomatic v0.36) to the published reference genome of g. oxydans using bowtie2 v2.2.7 [41, 42]. cufflinks and cuffnorm were used to quantify transcript levels [43]., detection of tsss was done with libraries enriched for primary transcripts using readxplorer [44] […]

Bowtie2 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
Bowtie2 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.

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