Bowtie protocols

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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


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  • person_outline Ben Langmead <>

Publication for Bowtie

Bowtie in pipelines

PMCID: 5752201
PMID: 29297464
DOI: 10.7554/eLife.29815.043

[…] contained all adapter and primer sequences from the truseq small rna sample preparation kit. subsequently, reads were aligned to saccharomyces cerevisiae genome ef4.72 from ensembl using bowtie version 1.0.0 (rrid:scr_005476) () with parameters ‘-n 0 –l 28 –e 70 –k1 –m 1 --best --strata --sam --nomaqround’. reads were counted per exon using htseq-count (rrid:scr_011867) () […]

PMCID: 5755174
PMID: 29301509
DOI: 10.1186/s12885-017-3945-6

[…] datasets used in this study are listed in supplementary additional file : table s9., raw reads were quality filtered and trimmed with fastx-toolkit ( bowtie v1.0.0 [] was used to align trimmed reads to hg38 human genome assembly with zero mismatches. alignment procedure was based on tailor aligner []. briefly, unaligned reads were trimmed by one […]

PMCID: 5761873
PMID: 29320577
DOI: 10.1371/journal.pone.0190485

[…] quality of generated reads was assessed using fastqc, a quality control tool., the reads after removal of 3/ adapters by cutadapt were aligned to the human reference genome and transcriptomes using bowtie, an efficient and widely used genome-scale alignment tool []. the uniquely mapped reads with no more than one mismatch in the alignment were considered for their annotations. the human […]

PMCID: 5764346
PMID: 29324804
DOI: 10.1371/journal.pone.0191081

[…] segments of sugarcane, with the different segments classified as base “zero” (b0), base (b), middle (m) and tip (t), according to matiello et al. []. the transcriptome was mapped using the program bowtie 2.0. the software rsem (rna-seq by expectation maximization) was used in de novo assembly to quantify the rna-seq reads self-normalized using fpkm values (mean fragments per kilobase […]

PMCID: 5771010
PMID: 29338737
DOI: 10.1186/s12985-018-0926-6

[…] if any read of the paired-end reads are adaptor-polluted. the assembler trinity was used for de novo assembly []. we quantified the proportion of the clean reads that mapped to each assembly using bowtie (v2.2.3). to test the completeness of the assemblies, we mapped the presence of highly conserved genes with 2748 core proteins from conserved regions of eukaryotes. transdecoder was used […]

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Bowtie in publications

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

[…] 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 […]

PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] sequencing on an illumina hiseq 2500 (illumina) by nyu genome technology center., atac-seq fastq files were quality trimmed using fastqc (v0.11.5) and mapped to the mouse genome (mm9) using bowtie (v2.2.6), using the default options. mapped sam files were sorted and converted to bam files with samtools (v0.1.19-96b5f2294a). accessible regions were determined using macs2 […]

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

[…] in r with q-value <0.05 for six marks., 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 […]

PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] as quantified using a line1 real-time pcr assay on a serial dilution of normal dna in each plate as standard., fastqc,; bowtie2 2.1.0,; picard tool markduplicates v1.97,; haplotypecaller, […]

PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] expression measurements. gene expression levels were measured using the rsem software (version 1.2.16) rsem was run on a merged fastq file for each sample, setting the ‘--bowtie2‘ flag and using bowtie version 2.1.0, the ‘--num-threads‘ flag to 8, and ‘--calc-ci‘ flag. the rsem reference was prepared using the rsem-prepare-reference executable with the same hg19 genome file as was used […]

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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.