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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 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

[…] 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 […]


B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

Nat Commun
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 […]


Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast like synoviocytes

Nat Commun
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 […]


Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

Nat Commun
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, […]


Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Nat Commun
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 […]


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

[…] were grouped into putative genome bins using a composition-independent differential coverage binning pipeline []. in brief, clean reads from mp and ap metagenomes were mapped independently with bowtie 2 (version 2.1.0) [] to scaffolds of mp metagenomes (≥ 95% identity over full length). the scaffolds were then visualized in an r plot (with scaffold coverages, gc content, and taxonomic […]

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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.