Fast gapped-read alignment with Bowtie 2.

PubWeight™: 83.79‹?› | Rank: Top 0.01% | All-Time Top 1000

🔗 View Article (PMC 3322381)

Published in Nat Methods on March 04, 2012

Authors

Ben Langmead1, Steven L Salzberg

Author Affiliations

1: Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA. blangmea@jhsph.edu

Articles citing this

(truncated to the top 100)

Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (2014) 44.23

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc (2013) 13.33

Diet rapidly and reproducibly alters the human gut microbiome. Nature (2013) 11.04

Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (2013) 8.81

Circular RNAs are a large class of animal RNAs with regulatory potency. Nature (2013) 8.54

IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res (2013) 6.14

PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics (2013) 5.61

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature (2014) 5.47

Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature (2014) 5.45

Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature (2014) 5.22

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature (2014) 5.19

The MaSuRCA genome assembler. Bioinformatics (2013) 5.07

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One (2014) 4.94

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res (2013) 4.45

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res (2014) 4.29

Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell (2015) 4.16

The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods (2012) 3.89

A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform (2013) 3.60

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol (2015) 3.56

Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods (2013) 3.52

TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One (2014) 3.45

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res (2014) 3.43

Absence of putative artemisinin resistance mutations among Plasmodium falciparum in Sub-Saharan Africa: a molecular epidemiologic study. J Infect Dis (2014) 3.21

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol (2012) 3.13

RNA-Seq gene profiling--a systematic empirical comparison. PLoS One (2014) 3.03

Landscape and variation of RNA secondary structure across the human transcriptome. Nature (2014) 3.01

IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res (2013) 2.99

Cell-type specific features of circular RNA expression. PLoS Genet (2013) 2.98

Human gut microbiota community structures in urban and rural populations in Russia. Nat Commun (2013) 2.95

Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods (2013) 2.92

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature (2015) 2.86

HISAT: a fast spliced aligner with low memory requirements. Nat Methods (2015) 2.83

Role of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia. Nature (2014) 2.79

A benchmark for RNA-seq quantification pipelines. Genome Biol (2016) 2.78

Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell (2014) 2.78

Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature (2013) 2.68

Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma. Nat Med (2014) 2.53

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med (2014) 2.51

Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res (2013) 2.50

Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat Neurosci (2012) 2.44

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol (2014) 2.44

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci U S A (2014) 2.42

Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature (2015) 2.41

Synthetic lethality by targeting EZH2 methyltransferase activity in ARID1A-mutated cancers. Nat Med (2015) 2.41

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nat Cell Biol (2013) 2.40

Redefining the invertebrate RNA virosphere. Nature (2016) 2.39

A survey of best practices for RNA-seq data analysis. Genome Biol (2016) 2.37

Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics (2014) 2.37

The ribonuclease activity of SAMHD1 is required for HIV-1 restriction. Nat Med (2014) 2.35

Unusual biology across a group comprising more than 15% of domain Bacteria. Nature (2015) 2.34

Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas. Nat Genet (2014) 2.34

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res (2013) 2.29

Differential L1 regulation in pluripotent stem cells of humans and apes. Nature (2013) 2.29

Biogeography and individuality shape function in the human skin metagenome. Nature (2014) 2.27

GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics (2013) 2.24

New CRISPR-Cas systems from uncultivated microbes. Nature (2016) 2.22

Aerobic glycolysis promotes T helper 1 cell differentiation through an epigenetic mechanism. Science (2016) 2.20

Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth. Nature (2015) 2.20

Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLoS Genet (2015) 2.19

Rapid evolutionary response to a transmissible cancer in Tasmanian devils. Nat Commun (2016) 2.19

Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation. Nature (2016) 2.17

The genetics of monarch butterfly migration and warning colouration. Nature (2014) 2.16

Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature (2017) 2.16

BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin. Nat Struct Mol Biol (2016) 2.15

Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature (2017) 2.14

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One (2014) 2.12

Synaptic dysregulation in a human iPS cell model of mental disorders. Nature (2014) 2.12

Effect of natural genetic variation on enhancer selection and function. Nature (2013) 2.10

Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics (2014) 2.07

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens. Science (2015) 2.06

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol (2016) 2.05

A quantitative comparison of single-cell whole genome amplification methods. PLoS One (2014) 2.04

The microbiome of uncontacted Amerindians. Sci Adv (2015) 2.04

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol (2015) 2.03

Middle East respiratory syndrome coronavirus quasispecies that include homologues of human isolates revealed through whole-genome analysis and virus cultured from dromedary camels in Saudi Arabia. MBio (2014) 2.02

Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol Cell (2013) 1.96

Somatic mosaicism and allele complexity induced by CRISPR/Cas9 RNA injections in mouse zygotes. Dev Biol (2014) 1.96

Multiple roles for Piwi in silencing Drosophila transposons. Genes Dev (2013) 1.96

A long noncoding RNA protects the heart from pathological hypertrophy. Nature (2014) 1.96

Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma. Nat Genet (2013) 1.93

SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol (2015) 1.93

Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods (2013) 1.92

Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc (2013) 1.91

Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML. Cell (2016) 1.91

Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. Science (2015) 1.91

EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biol (2013) 1.90

Strand-specific analysis shows protein binding at replication forks and PCNA unloading from lagging strands when forks stall. Mol Cell (2014) 1.90

Identification, characterization, and in vitro culture of highly divergent arenaviruses from boa constrictors and annulated tree boas: candidate etiological agents for snake inclusion body disease. MBio (2012) 1.90

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods (2015) 1.88

The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature (2016) 1.88

Polyploidy can drive rapid adaptation in yeast. Nature (2015) 1.87

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature (2015) 1.86

Numerous transitions of sex chromosomes in Diptera. PLoS Biol (2015) 1.85

A neural basis for melanocortin-4 receptor-regulated appetite. Nat Neurosci (2015) 1.85

Computational meta'omics for microbial community studies. Mol Syst Biol (2013) 1.84

A Gpr120-selective agonist improves insulin resistance and chronic inflammation in obese mice. Nat Med (2014) 1.83

Multicilin drives centriole biogenesis via E2f proteins. Genes Dev (2014) 1.82

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics (2014) 1.82

T cell fate and clonality inference from single-cell transcriptomes. Nat Methods (2016) 1.81

Articles by these authors

(truncated to the top 100)

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12

TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21

Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45

Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63

Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42

The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31

FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71

Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52

Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature (2005) 11.99

The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03

The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature (2003) 10.38

Searching for SNPs with cloud computing. Genome Biol (2009) 10.12

Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (2002) 9.83

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43

Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods (2009) 8.15

Cloud computing and the DNA data race. Nat Biotechnol (2010) 7.81

Minimus: a fast, lightweight genome assembler. BMC Bioinformatics (2007) 7.65

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science (2005) 7.61

How to map billions of short reads onto genomes. Nat Biotechnol (2009) 6.59

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol (2011) 6.23

Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature (2008) 5.96

The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94

Assembly of large genomes using second-generation sequencing. Genome Res (2010) 5.94

A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol (2009) 5.93

The genome of woodland strawberry (Fragaria vesca). Nat Genet (2010) 5.86

Comparative genome assembly. Brief Bioinform (2004) 5.81

Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54

Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol (2005) 5.48

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44

Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol (2014) 5.40

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39

Comparative genomics of trypanosomatid parasitic protozoa. Science (2005) 5.37

Bioinformatics challenges of new sequencing technology. Trends Genet (2008) 5.34

Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28

The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A (2002) 5.28

The MaSuRCA genome assembler. Bioinformatics (2013) 5.07

Hierarchical scaffolding with Bambus. Genome Res (2004) 4.95

Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol (2002) 4.90

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89

Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biol (2007) 4.80

The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (2005) 4.74

Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol (2007) 4.27

Beware of mis-assembled genomes. Bioinformatics (2005) 4.14

DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics (2004) 3.74

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73

Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics (2003) 3.50

Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics (2010) 3.38

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol (2004) 3.36

Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (2005) 2.71

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc Natl Acad Sci U S A (2011) 2.62

Computational gene prediction using multiple sources of evidence. Genome Res (2004) 2.58

The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol (2002) 2.58

Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature (2002) 2.49

JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics (2005) 2.37

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol (2004) 2.36

GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics (2013) 2.24

Physiogenomic resources for rat models of heart, lung and blood disorders. Nat Genet (2006) 2.05

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. Genome Biol (2006) 2.00

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol (2014) 1.90

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. J Bacteriol (2011) 1.80

Automated correction of genome sequence errors. Nucleic Acids Res (2004) 1.80

Comprehensive DNA signature discovery and validation. PLoS Comput Biol (2007) 1.75

Between a chicken and a grape: estimating the number of human genes. Genome Biol (2010) 1.72

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res (2010) 1.72

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform (2011) 1.70

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Res (2003) 1.63

The complete genome sequence of Bacillus anthracis Ames "Ancestor". J Bacteriol (2008) 1.61

Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biol (2010) 1.54

The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol (2003) 1.52

Computational discovery of internal micro-exons. Genome Res (2003) 1.52

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res (2005) 1.48

OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res (2008) 1.47

Sequencing and assembly of the 22-gb loblolly pine genome. Genetics (2014) 1.46

What are decision trees? Nat Biotechnol (2008) 1.39

2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates. PLoS One (2009) 1.32

Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics (2014) 1.32

Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J Bacteriol (2010) 1.29

Computational gene finding in plants. Plant Mol Biol (2002) 1.29

Clustering metagenomic sequences with interpolated Markov models. BMC Bioinformatics (2010) 1.28

The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24

Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Res (2009) 1.23

Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas. PLoS One (2008) 1.22

A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biol Direct (2014) 1.20

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res (2011) 1.17

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics (2010) 1.14

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics (2007) 1.13

Do-it-yourself genetic testing. Genome Biol (2010) 1.06

Efficient decoding algorithms for generalized hidden Markov model gene finders. BMC Bioinformatics (2005) 1.05

Contamination in the draft of the human genome masquerades as lateral gene transfer. DNA Seq (2002) 1.00