Bowtie2 statistics

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Citations per year

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Popular tool citations

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Associated diseases

Associated diseases


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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

[…] to the human genome hg19 using tophat. unmapped reads were filtered out. transcripts were assembled by cufflink. differential expression of transcripts was estimated by cuffdiff . 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) [] and for each gene cluster, the number of mapped […]

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 [, ]. reads overlapping with the annotation range of interest were counted for each sample using the “summarizeoverlaps” function []. read counting was performed for exonic gene regions […]

PMCID: 5754362
PMID: 29302059
DOI: 10.1038/s41467-017-02512-1

[…] data were analyzed as outlined above for rna-seq., to study chromatin transitions by chip-seq analysis, sequences were filtered using trimmomatic and mapped to the rn6 reference rat genome using the bowtie2 aligner as described above (rna-seq data analysis). to identify the regions of the genome enriched in h3k27ac and h3k4me1, we visualized the alignment of mapped reads using the integrated […]

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Bowtie2 in publications

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18

[…] using megan6 community edition (). an extra contaminant file was created with the complete genomes of species present at over 1,000 reads in the positive- and negative-control samples. then, bowtie2 () was used for each sample to subtract the reads that mapped to the positive-control, negative-control, or contaminant file. the unmapped reads were used for assembly with spades version […]

PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z

[…] lower read qualities in those bases as compared to the remainder of the read. trimmed reads that passed the trimmomatic selection criteria were then aligned to the rn6 build of the rat genome with bowtie2/tophat2, using default parameters. aligned reads were assigned to gene-level genomic features of the ensembl 83 annotation set using the rsubread featurecounts r function […]

PMCID: 5955981
PMID: 29769661
DOI: 10.1038/s41598-018-26065-5

[…] (small rna). after pcr amplification, the final libraries were quantitated by qpcr (kapa library quant kit, kapa biosystems)., read counts (expression levels) were obtained using a pipeline based on bowtie2 as alignment tool and the read count were determined using rna-seq by expectation maximization (rsem)., micrornas with less than 10 counts in more than 90% of the samples were excluded. […]

PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] in rapid run mode at the duke gcb sequencing shared resource. reads were aligned to a combinational genome consisting of the human reference genome hg19 and the drosophila reference genome dm6 using bowtie2. alignment files were then filtered according to their alignment scores and down-sampled to ensure each file contains the same amount of unique drosophila reads. finally, reads mapped to hg19 […]

PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] data was performed using fastqc before and after adaptor trimming with trimmomatic (). then, the paired-end reads were assembled using pandaseq and aligned to the hg38 genome assembly using bowtie2 (, ). finally, the total mature mirna counts were generated with htseq (). we removed 7 samples (s01, s02, s03, s36, s40, s41, s43) due to a low number of total raw reads (fewer than 500,000 […]

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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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