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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




No version available


  • person_outline Benjamin Langmead

Additional information

Publication for Bowtie2

Bowtie2 citations


Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] sualized 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 3.9. […]


Elucidating the genetic architecture of reproductive ageing in the Japanese population

Nat Commun
PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z
call_split See protocol

[…] ly 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 with countMultiMappin […]


Circulating MiR 374a 5p is a potential modulator of the inflammatory process in obesity

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

[…] ts (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. The data […]


Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width

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

[…] TQ format for the TF ChIP-seq experiments were downloaded using the accession numbers in Supplementary Fig.  and B, aligned to the reference genome hg19 for HCT116 cells and mm8 for mouse liver using Bowtie2, and filtered according to alignment scores using SAMtools. SRA files were converted to FASTQ format using the command fastq-dump in the SRA Toolkit ( before […]


DOT1L inhibition attenuates graft versus host disease by allogeneic T cells in adoptive immunotherapy models

Nat Commun
PMCID: 5954061
PMID: 29765028
DOI: 10.1038/s41467-018-04262-0
call_split See protocol

[…] ed on a Phred quality score >20 and read lengths >30 using the FASTX Toolkit (version 0.0.14), and the trimmed reads were mapped to the GRCh37 human reference genome using TopHat (version 2.0.14) and Bowtie2 (version 2.2.9). The read counts and FPKM values for each gene were calculated using Cufflinks (v2.1.1). The log2-transformed (FPKM+1) values were compared between SGC0946- and DMSO-treated T […]


Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

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

[…] equencing 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 r […]


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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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