Bowtie statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


Bowtie specifications


Unique identifier OMICS_00653
Name Bowtie
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
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




No version available



  • person_outline Ben Langmead

Publication for Bowtie

Bowtie citations


Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells

Sci Rep
PMCID: 5958073
PMID: 29773913
DOI: 10.1038/s41598-018-25963-y

[…] s were analyzed. The produced bcl files were converted to fastq files by bcl2fastq (Illumina). The reads were analyzed as previously described and were mapped to the Arabidopsis reference (TAIR10) by bowtie 1.2.1 with the following parameters: ‘-all -best -strata’ (Table ). The number of reads mapped to each reference was counted. The sequencing data are deposited at DDBJ (accession number DRA0057 […]


Genomic alterations of ground glass nodular lung adenocarcinoma

Sci Rep
PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] apped to the reference human genome (hg19) using TopHat. Then unmapped reads were chosen and were converted into the FASTQ format. They were mapped with zero mismatch to 6,251 viral genomes using the Bowtie tool ( Mapped read counts were compared between normal and tumor samples. […]


Integrated analysis of hepatic mRNA and miRNA profiles identified molecular networks and potential biomarkers of NAFLD

Sci Rep
PMCID: 5955949
PMID: 29769539
DOI: 10.1038/s41598-018-25743-8

[…] sis, adaptor sequence trimming and removal of low-quality reads were performed. Clean reads were aligned with the rat genome using TopHat v2.1.1. Based on the ultra-high throughput short-read aligner Bowtie, TopHat aligned RNA-Seq reads to reference genomes and analyzed the mapping reads to determine possible splice junctions between exons. RNA expression levels were determined by reads per kiloba […]


Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast like synoviocytes

Nat Commun
PMCID: 5953939
PMID: 29765031
DOI: 10.1038/s41467-018-04310-9

[…] ATAC-seq sample preparation was followed by previous protocol and was sequenced by Epinomics (San Francisco, CA). ATAC-seq data were processed using Bowtie and read depth was normalized. ATAC-seq DMERs were determined by DiffBind package in R with q-value <0.05. The bisulfite conversion and sequencing were performed by GATC Biotech AG (Germany). W […]


The novel 19q13 KRAB zinc finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/β catenin signalling

PMCID: 5951945
PMID: 29760376
DOI: 10.1038/s41419-018-0604-z
call_split See protocol

[…] re prepared using a NEBNext Ultra RNA LibraryPrep Kit for Illumina (New England Biolabs) following the manufacturer’s recommendations. RNA-Seq was performed with an Illumina Hiseq 2000/2500 platform. Bowtie v. 2.0.6– and TopHat v. 2.0.9– were used for reads mapping to the reference genome. Genes with an adjusted p or0.05 and identified with DESeq, were considered to be differentially expressed. […]


Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome resolved metagenomics

Biotechnol Biofuels
PMCID: 5946492
PMID: 29774049
DOI: 10.1186/s13068-018-1136-6

[…] The abundance of reconstructed genomes was calculated as the number of metagenomic reads mapped to each curated genome divided by the total number of reads in the metagenome using Bowtie 2 with default parameters. In total, 107 essential single-copy marker genes (ESCGs) and 35 conserved clusters of orthologous groups (COG) markers were used for estimates of completeness and pot […]


Looking to check out a full list of citations?

Bowtie institution(s)
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
Bowtie funding source(s)
Supported in part by NIH grants R01-LM006845 and R01-GM083873.

Bowtie reviews

star_border star_border star_border star_border star_border
star star star star star

clement GARCIA

star_border star_border star_border star_border star_border
star star star star star
Great tools for read mapper

Arup Ghosh

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