Bowtie pipeline

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



Add your version



  • person_outline Ben Langmead <>

Publication for Bowtie

Bowtie IN pipelines

PMCID: 5762668
PMID: 29321689
DOI: 10.1038/s41598-017-18675-2

[…] were obtained using the illumina casava pipeline (version 1.8)., to analyze the rna-seq data from human smcs and ecs, we used hg19 (human genome version 19, ucsc) as the human reference genome. a bowtie 213 index was built, and tophat214 was used to align transcripts to the annotated human genome, and transcriptomes were then assembled using cufflinks 2.015., the cuffdiff program […]

PMCID: 5768803
PMID: 29335477
DOI: 10.1038/s41598-017-17735-x

[…] isolated using magnetic purification. single-end read sequencing was performed using an illumina hiseq. 2000. sequencing reads were aligned to the human genome build 37.1 using tophat (1.3.3) and bowtie (0.12.7). quality control and normalization of the mrna-sequencing gene counts data are as described by ovsyannikova et al.51 briefly, gene counts were normalized using conditional quantile […]

PMCID: 5773744
PMID: 29348359
DOI: 10.1128/genomeA.01507-17

[…] usa) were assembled using canu version 1.4 (4). after circularization, ion torrent reads (3,351,349 reads) (thermo fisher, usa) were mapped against the contig from the pacbio assembly using bowtie 2 version 2.2.4 (5). to spot possible frameshifts, single nucleotide variants were called using samtools version 1.3 (6), and the errors were corrected manually with the visual aid of geneious […]

PMCID: 5778647
PMID: 29357872
DOI: 10.1186/s12977-018-0394-5

[…] ( and reads shorter than 25 nt following adaptor trimming were discarded. trimmed reads were then mapped to host (rattus norvegicus) and virus rna using bowtie version 1 [38], with parameters-v 2—best (i.e. maximum 2 mismatches, report best match). mapping was performed in the following order: host rrna; virus rna; host refseq mrna; host non-coding […]

PMCID: 5785540
PMID: 29371665
DOI: 10.1038/s41467-017-02740-5

[…] 20752) as described24. chip-seq libraries were prepared, sequenced using the standard illumina protocol (hiseq2000, single read, 50 bp v3), and mapped to the mouse mm10 reference genome by bowtie45. data were further analyzed using the peak finding algorithm macs 1.4.246. homer software was used to annotate peaks47, and all peaks with false discovery rate <1% were included. […]

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

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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.