Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

doi:10.1186/gb-2009-10-3-r25

PMID: 19261174DOI: 10.1186/gb-2009-10-3-r25Mar 6, 2009Paper

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Genome Biology

Ben LangmeadSteven L Salzberg

Abstract

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu).

Associated Clinical Trials

Cardiac Allograft Remodeling and Effects of Sirolimus

Jul 1, 2013

References

Identification of common molecular subsequences

Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman

Base-calling of automated sequencer traces using phred. II. Error probabilities

May 16, 1998·Genome Research·B Ewing, P Green

PatternHunter: faster and more sensitive homology search

Apr 6, 2002·Bioinformatics·Bin MaMing Li

Annotating large genomes with exact word matches

Sep 17, 2003·Genome Research·John HealyMichael Wigler

Space-efficient whole genome comparisons with Burrows-Wheeler transforms

May 11, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ross A Lippert

Genome-wide mapping of in vivo protein-DNA interactions

Jun 2, 2007·Science·David S JohnsonBarbara Wold

Optimized design and assessment of whole genome tiling arrays

Jul 25, 2007·Bioinformatics·Stefan GräfPaul Flicek

SeqAn an efficient, generic C++ library for sequence analysis

Jan 11, 2008·BMC Bioinformatics·Andreas DöringKnut Reinert

DNA sequencing. A plan to capture human diversity in 1000 genomes

Jan 26, 2008·Science·Jocelyn Kaiser

SOAP: short oligonucleotide alignment program

Jan 30, 2008·Bioinformatics·Ruiqiang LiJun Wang

Compressed indexing and local alignment of DNA

Jan 30, 2008·Bioinformatics·T W LamS M Yiu

Using quality scores and longer reads improves accuracy of Solexa read mapping.

Mar 1, 2008·BMC Bioinformatics·Andrew D SmithMichael Q Zhang

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

Apr 29, 2008·Nature Genetics·Peter J CampbellP Andrew Futreal

The transcriptional landscape of the yeast genome defined by RNA sequencing.

May 3, 2008·Science·Ugrappa NagalakshmiMichael Snyder

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.

Jun 14, 2008·Genome Research·John C MarioniYoav Gilad

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Jul 10, 2008·Nature Biotechnology·Thomas A DownStephan Beck

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

Jul 29, 2008·Nature Genetics·Kathryn E HoltGordon Dougan

ZOOM! Zillions of oligos mapped.

Aug 8, 2008·Bioinformatics·Hao LinMing Li

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Aug 21, 2008·Genome Research·Heng LiRichard Durbin

Accurate whole human genome sequencing using reversible terminator chemistry

Nov 7, 2008·Nature·David R BentleyAnthony J Smith

The diploid genome sequence of an Asian individual

Nov 7, 2008·Nature·Jun WangJian Wang

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Nov 7, 2008·Nature·Timothy J LeyRichard K Wilson

❮ Previous

Next ❯

Citations

RNA-seq: from technology to biology.

Oct 28, 2009·Cellular and Molecular Life Sciences : CMLS·Samuel Marguerat, Jürg Bähler

Genomic inversion caused by gamma irradiation contributes to downregulation of a WBC11 homolog in bloomless sorghum

Mar 7, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hiroshi MizunoTakashi Matsumoto

Fine mapping and chromosome walking towards the Ror1 locus in barley (Hordeum vulgare L.)

Sep 18, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Johanna Acevedo-GarciaRalph Panstruga

High-throughput sequencing of frozen and paraffin-embedded tumor and normal tissue

Sep 3, 2010·Der Pathologe·M KerickM-R Schweiger

Pollen transcriptome analysis of Solanum tuberosum (2n = 4x = 48), S. demissum (2n = 6x = 72), and their reciprocal F1 hybrids

Feb 23, 2013·Plant Cell Reports·Rena Sanetomo, Kazuyoshi Hosaka

Condensin dysfunction in human cells induces nonrandom chromosomal breaks in anaphase, with distinct patterns for both unique and repeated genomic regions

Dec 20, 2011·Chromosoma·Alexander SamoshkinAlexander V Strunnikov

Evolution of GOLDEN2-LIKE gene function in C(3) and C (4) plants.

Sep 13, 2012·Planta·Peng WangJane A Langdale

An EST dataset for Metasequoia glyptostroboides buds: the first EST resource for molecular genomics studies in Metasequoia

Nov 3, 2012·Planta·Ying ZhaoHaiying Liang

A genomewide survey of bHLH transcription factors in the coral Acropora digitifera identifies three novel orthologous families, pearl, amber, and peridot.

Mar 16, 2012·Development Genes and Evolution·Fuki GyojaNori Satoh

Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette.

Oct 12, 2012·Development Genes and Evolution·Nathan J Kenny, Sebastian M Shimeld

Hyperuricemia cosegregating with osteogenesis imperfecta is associated with a mutation in GPATCH8.

May 20, 2011·Human Genetics·Hiroshi KanekoKinji Ohno

A beginners guide to SNP calling from high-throughput DNA-sequencing data.

Aug 14, 2012·Human Genetics·André AltmannBertram Müller-Myhsok

Using small RNA sequences to diagnose, sequence, and investigate the infectivity characteristics of vegetable-infecting viruses

Mar 31, 2011·Archives of Virology·Charles HagenShihshieh Huang

A novel miRNA produced during lytic HSV-1 infection is important for efficient replication in tissue culture

Jun 5, 2012·Archives of Virology·Daniel J Munson, April D Burch

Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells.

Jan 18, 2012·Functional & Integrative Genomics·Joo Heon ShinCong-jun Li

Copy number variation in the cattle genome

Jul 14, 2012·Functional & Integrative Genomics·George E Liu, Derek M Bickhart

Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice

Feb 20, 2013·Functional & Integrative Genomics·Fangqian Ou-YangChristopher D Rock

Identification of mediator complex 26 (Crsp7) gametologs on platypus X1 and Y5 sex chromosomes: a candidate testis-determining gene in monotremes?

Jan 5, 2012·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Enkhjargal Tsend-AyushFrank Grützner

MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis

Jan 24, 2013·Plant Molecular Biology·Fan Jia, Christopher D Rock

Deep RNA-Seq uncovers the peach transcriptome landscape

Jun 21, 2013·Plant Molecular Biology·Lu WangYuepeng Han

Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing

Jul 19, 2013·Plant Molecular Biology·Xin QiJingjuan Yu

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles

Jul 17, 2013·Plant Molecular Biology·Youko OonoTakashi Matsumoto

Genome-wide identification of cancer-related polyadenylated and non-polyadenylated RNAs in human breast and lung cell lines

May 15, 2013·Science China. Life Sciences·Guoguang ZhaoRunsheng Chen

Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA.

Mar 14, 2013·Symbiosis·Sandrine GeniezBarton E Slatko

First insights into the metagenome of Egyptian mummies using next-generation sequencing

Apr 5, 2013·Journal of Applied Genetics·Rabab KhairatCarsten M Pusch

Transcriptomic analysis of cultured whale skin cells exposed to hexavalent chromium [Cr(VI)

Apr 16, 2013·Aquatic Toxicology·Vagmita PabuwalRonald B Walter

Transcriptome profiling and genome-wide DNA binding define the differential role of fenretinide and all-trans RA in regulating the death and survival of human hepatocellular carcinoma Huh7 cells

Feb 12, 2013·Biochemical Pharmacology·Ying HuYu-Jui Yvonne Wan

Macrohistone variants preserve cell identity by preventing the gain of H3K4me2 during reprogramming to pluripotency

Apr 3, 2013·Cell Reports·María J BarreroJuan Carlos Izpisua Belmonte

Weight loss after gastric bypass surgery in human obesity remodels promoter methylation

Apr 16, 2013·Cell Reports·Romain BarresJuleen R Zierath

Placing the HIRA histone chaperone complex in the chromatin landscape

Apr 23, 2013·Cell Reports·Nikolay A PchelintsevPeter D Adams

Mapping of mitochondrial RNA-protein interactions by digital RNase footprinting

Nov 5, 2013·Cell Reports·Ganqiang LiuAleksandra Filipovska

Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage.

Sep 3, 2011·Cell Stem Cell·Wen-Hui LienElaine Fuchs

Finding the lost treasures in exome sequencing data

Aug 27, 2013·Trends in Genetics : TIG·David C SamuelsYan Guo

RNA-Seq: revelation of the messengers

Mar 14, 2013·Trends in Plant Science·Marcel C Van VerkSaskia C M Van Wees

Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts

Mar 19, 2013·Genetics Research·E PurdomI Haviv

Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK

Feb 22, 2013·Epidemiology and Infection·J McDonnellC Jenkins

Maternal separation with early weaning: a rodent model providing novel insights into neglect associated developmental deficits.

Oct 16, 2012·Development and Psychopathology·Becky C CarlyleArthur A Simen

Age-related changes of gene expression in the neocortex: preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas.

Oct 16, 2012·Development and Psychopathology·Oksana Yu NaumovaElena L Grigorenko

The integration of 'omic' disciplines and systems biology in cattle breeding

Mar 24, 2012·Animal : an International Journal of Animal Bioscience·D P BerryC J Creevey

Improved sensitivity of DNA microarrays using photonic crystal enhanced fluorescence.

Aug 14, 2010·Analytical Chemistry·Patrick C MathiasBrian T Cunningham

Using genetic methods to define the targets of compounds with antimalarial activity

Aug 10, 2013·Journal of Medicinal Chemistry·Erika L FlanneryElizabeth A Winzeler

Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment

Jan 6, 2012·Journal of Proteome Research·Surendra DasariDavid L Tabb

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization.

Jan 25, 2012·Cell Research·Iouri ChepelevKeji Zhao

Defining the expressed breast cancer kinome.

Feb 9, 2012·Cell Research·Alicia A MidlandGary L Johnson

Haploinsufficiency of CELF4 at 18q12.2 is associated with developmental and behavioral disorders, seizures, eye manifestations, and obesity.

May 24, 2012·European Journal of Human Genetics : EJHG·Christina HalgrenNiels Tommerup

WITHDRAWN: Evaluation of next-generation sequencing software in mapping and assembly

Jun 17, 2011·Journal of Human Genetics·Suying BaoYou-Qiang Song

Comparative genomic integration profiling of Sleeping Beauty transposons mobilized with high efficacy from integrase-defective lentiviral vectors in primary human cells.

Apr 7, 2011·Molecular Therapy : the Journal of the American Society of Gene Therapy·Brian MoldtJacob Giehm Mikkelsen

A Hyperactive Transposase Promotes Persistent Gene Transfer of a piggyBac DNA Transposon

Jan 25, 2013·Molecular Therapy. Nucleic Acids·Erin R BurnightPaul B McCray

Human DNA methylomes at base resolution show widespread epigenomic differences.

Oct 16, 2009·Nature·Ryan ListerJoseph R Ecker

Mammalian microRNAs predominantly act to decrease target mRNA levels.

Aug 13, 2010·Nature·Huili GuoDavid P Bartel

❮ Previous

Next ❯

Datasets Mentioned

SRR001115

SRR003084

SRR003092

SRR003196

Software Mentioned

pthreads

Bowtie

Eland

UNPERMUTE

EXACTMATCH

RMAP

SOAP

ZOOM

PHRED

Maq

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.