Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
* Corresponding author: Ben Langmead langmead@cs.umd.edu
Genome Biology 2009, 10:R25 doi:10.1186/gb-2009-10-3-r25
Accesses
- Last 30 days: 2350 accesses
- Last year: 26701 accesses
- All time: 71646 accesses
Cited by
BioMed Central: 79 citations
|
Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy Yanni Sun, Osama Aljawad, Jikai Lei, Alex Liu BMC Bioinformatics 2012, 13(Suppl 3):S12 (21 March 2012) |
|
Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynanen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R Steffensen, Carsten Carlberg BMC Genomics 2012, 13:50 (31 January 2012) |
|
BarraCUDA - a fast short read sequence aligner using graphics processing units Petr Klus, Simon Lam, Dag Lyberg, Ming Sin Cheung, Graham Pullan, Ian McFarlane, Giles S H Yeo, Brian Y H Lam BMC Research Notes 2012, 5:27 (13 January 2012) |
|
Peter Arensburger, Robert H Hice, Jennifer A Wright, Nancy L Craig, Peter W Atkinson BMC Genomics 2011, 12:606 (15 December 2011) |
|
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study Qiong-Yi Zhao, Yi Wang, Yi-Meng Kong, Da Luo, Xuan Li, Pei Hao BMC Bioinformatics 2011, 12(Suppl 14):S2 (14 December 2011) |
|
Revealing the missing expressed genes beyond the human reference genome by RNA-Seq Geng Chen, Ruiyuan Li, Leming Shi, Junyi Qi, Pengzhan Hu, Jian Luo, Mingyao Liu, Tieliu Shi BMC Genomics 2011, 12:590 (2 December 2011) |
|
Robert W Li, Manuela Rinaldi, Anthony V Capuco Veterinary Research 2011, 42:114 (30 November 2011) |
|
UASIS: Universal Automatic SNP Identification System Danny C C Poo, Shaojiang Cai, James T L Mah BMC Genomics 2011, 12(Suppl 3):S9 (30 November 2011) |
|
Perfect Hamming code with a hash table for faster genome mapping Yoichi Takenaka, Shigeto Seno, Hideo Matsuda BMC Genomics 2011, 12(Suppl 3):S8 (30 November 2011) |
|
Next-generation sequencing technologies and applications for human genetic history and forensics Eva C Berglund, Anna Kiialainen, Ann-Christine Syvänen Investigative Genetics 2011, 2:23 (24 November 2011) |
|
Identification and correction of systematic error in high-throughput sequence data Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David IK Martin, Meromit Singer, Lior Pachter BMC Bioinformatics 2011, 12:451 (21 November 2011) |
|
Robert M Givens, Larry D Mesner, Joyce L Hamlin, Michael J Buck, Joel A Huberman BMC Research Notes 2011, 4:499 (16 November 2011) |
|
Xiaowei S Chen, David Penny, Lesley J Collins BMC Genomics 2011, 12:550 (6 November 2011) |
|
RNA-Seq improves annotation of protein-coding genes in the cucumber genome Zhen Li, Zhonghua Zhang, Pengcheng Yan, Sanwen Huang, Zhangjun Fei, Kui Lin BMC Genomics 2011, 12:540 (2 November 2011) |
|
Transcript profiling reveals expression differences in wild-type and glabrous soybean lines Matt Hunt, Navneet Kaur, Martina Stromvik, Lila Vodkin BMC Plant Biology 2011, 11:145 (26 October 2011) |
|
David Sims, Ana M Mendes-Pereira, Jessica Frankum, Darren Burgess, Maria-Antonietta Cerone, Cristina Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J Lord Genome Biology 2011, 12:R104 (21 October 2011) The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method
|
|
Jun Odawara, Akihito Harada, Tomohiko Yoshimi, Kazumitsu Maehara, Taro Tachibana, Seiji Okada, Koichi Akashi, Yasuyuki Ohkawa BMC Genomics 2011, 12:516 (20 October 2011) |
|
The draft genome and transcriptome of Cannabis sativa Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011) The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
|
|
Transcriptome map of mouse isochores Stilianos Arhondakis, Kimon Frousios, Costas S Iliopoulos, Solon P Pissis, German Tischler, Sophia Kossida BMC Genomics 2011, 12:511 (17 October 2011) |
|
Matthew G Links, Eric Holub, Rays HY Jiang, Andrew G Sharpe, Dwayne Hegedus, Elena Beynon, Dean Sillito, Wayne E Clarke, Shihomi Uzuhashi, Mohammad H Borhan BMC Genomics 2011, 12:503 (13 October 2011) |
|
Establishing the baseline level of repetitive element expression in the human cortex Svitlana Tyekucheva, Robert H Yolken, W McCombie, Jennifer Parla, Melissa Kramer, Sarah J Wheelan, Sarven Sabunciyan BMC Genomics 2011, 12:495 (10 October 2011) |
|
Chung-Il An, Yao Dong, Nobuko Hagiwara BMC Developmental Biology 2011, 11:59 (10 October 2011) |
|
Dario Cantu, Stephen P Pearce, Assaf Distelfeld, Michael W Christiansen, Cristobal Uauy, Eduard Akhunov, Tzion Fahima, Jorge Dubcovsky BMC Genomics 2011, 12:492 (7 October 2011) |
|
Özgen Deniz, Oscar Flores, Federica Battistini, Alberto Pérez, Montserrat Soler-López, Modesto Orozco BMC Genomics 2011, 12:489 (7 October 2011) |
|
Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data Iros Barozzi, Alberto Termanini, Saverio Minucci, Gioacchino Natoli Biology Direct 2011, 6:51 (6 October 2011) Fish the ChIPs is a computational pipeline for complete ChIP-Seq data analysis of unlimited samples; it can be run on any Unix machine while providing a graphic interface for Mac.
|
|
STELLAR: fast and exact local alignments Birte Kehr, David Weese, Knut Reinert BMC Bioinformatics 2011, 12(Suppl 9):S15 (5 October 2011) |
|
Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis Tejasvi S Niranjan, Abby Adamczyk, Héctor Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry, Tao Wang Genome Biology 2011, 12:R93 (28 September 2011) Two methods are presented, SRFIM and SERVIC4E, for detecting rare variants in pooled exome samples
|
|
Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis Jaime I Davila, Maria P Arrieta-Montiel, Yashitola Wamboldt, Jun Cao, Joerg Hagmann, Vikas Shedge, Ying-Zhi Xu, Detlef Weigel, Sally A Mackenzie BMC Biology 2011, 9:64 (27 September 2011) |
|
Cyrille Saintenac, Dayou Jiang, Eduard D Akhunov Genome Biology 2011, 12:R88 (14 September 2011) Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat
|
|
Expanding whole exome resequencing into non-human primates Eric J Vallender Genome Biology 2011, 12:R87 (14 September 2011) Human DNA capture tools are used to capture and sequence non-human primate DNA
|
|
WebMGA: a customizable web server for fast metagenomic sequence analysis Sitao Wu, Zhengwei Zhu, Liming Fu, Beifang Niu, Weizhong Li BMC Genomics 2011, 12:444 (7 September 2011) |
|
Tobias Mourier BMC Genomics 2011, 12:440 (1 September 2011) |
|
Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:R81 (19 August 2011) This article is part of a collection on The tammar wallaby genome... The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
|
|
SAMQA: error classification and validation of high-throughput sequenced read data Thomas Robinson, Sarah Killcoyne, Ryan Bressler, John Boyle BMC Genomics 2011, 12:419 (18 August 2011) |
|
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data David L Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca L Skalsky, Jack D Keene, Uwe Ohler Genome Biology 2011, 12:R79 (18 August 2011) A method for identifying RNA binding sites and miRNA target motifs from PAR-CLIP data
|
|
The head-regeneration transcriptome of the planarian Schmidtea mediterranea Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer Genome Biology 2011, 12:R76 (16 August 2011) Next generation sequencing was used to investigate the transcriptome of head regeneration in the planarian Schmidtea mediterranea
|
|
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts Daehwan Kim, Steven L Salzberg Genome Biology 2011, 12:R72 (11 August 2011) A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm
|
|
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome Bo Li, Colin N Dewey BMC Bioinformatics 2011, 12:323 (4 August 2011) RSEM is a new user-friendly software tool for quantifying transcript abundance from RNA-seq data that does not rely on a reference genome and is particularly useful for quantification with de novo transcriptome assemblies
|
|
Addressing challenges in the production and analysis of illumina sequencing data Martin Kircher, Patricia Heyn, Janet Kelso BMC Genomics 2011, 12:382 (29 July 2011) Janet Kelso and colleagues review the potential problems and suggested solutions for users of Illumina sequencers, including general principles for library preparation, image analysis, run parameters and handling of sequences containing adapter chimeras.
|
|
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data Brad A Friedman, Tom Maniatis Genome Biology 2011, 12:R69 (28 July 2011) A web-based RNA-seq and microarray analysis tool
|
|
A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data Yufeng Shen, Yiwei Gu, Itsik Pe’er BMC Bioinformatics 2011, 12(Suppl 6):S4 (28 July 2011) |
|
Assembly of non-unique insertion content using next-generation sequencing Nathaniel Parrish, Farhad Hormozdiari, Eleazar Eskin BMC Bioinformatics 2011, 12(Suppl 6):S3 (28 July 2011) |
|
Hyunsoo Kim, Yingtao Bi, Sharmistha Pal, Ravi Gupta, Ramana V Davuluri BMC Bioinformatics 2011, 12:305 (27 July 2011) |
|
Applications of the pipeline environment for visual informatics and genomics computations Ivo D Dinov, Federica Torri, Fabio Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A Knowles, Andrew P Clark, John D Van Horn, Joseph Ames, Carl Kesselman, Arthur W Toga BMC Bioinformatics 2011, 12:304 (26 July 2011) |
|
Identification of genomic indels and structural variations using split reads Zhengdong D Zhang, Jiang Du, Hugo Lam, Alex Abyzov, Alexander E Urban, Michael Snyder, Mark Gerstein BMC Genomics 2011, 12:375 (25 July 2011) A new method for the identification of structural variations and indels based on split reads in short read sequencing allows discovery of the precise location and sequence of structural variants covering the whole size spectrum.
|
|
Prabin Bajgain, Bryce A Richardson, Jared C Price, Richard C Cronn, Joshua A Udall BMC Genomics 2011, 12:370 (18 July 2011) |
|
A comparative analysis of DNA methylation across human embryonic stem cell lines Pao-Yang Chen, Suhua Feng, Jong Joo, Steve E Jacobsen, Matteo Pellegrini Genome Biology 2011, 12:R62 (6 July 2011) A comparison of DNA methylation in three human embryonic stem cell lines
|
|
Melissa ML Wong, Charles H Cannon, Ratnam Wickneswari BMC Genomics 2011, 12:342 (5 July 2011) |
|
SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data Xutao Deng BMC Bioinformatics 2011, 12:267 (29 June 2011) |
|
Roberto A Barrero, Gabriel Keeble-Gagnère, Bing Zhang, Paula Moolhuijzen, Kazuho Ikeo, Yoshio Tateno, Takashi Gojobori, Felix D Guerrero, Ala Lew-Tabor, Matthew Bellgard BMC Genomics 2011, 12:328 (24 June 2011) Anciently acquired microRNAs, discovered in the cattle tick Rhipicephalus microplus, tend to be highly conserved and ubiquitously expressed across tissues and life stages when compared to newly acquired tick-specific miRNAs.
|
|
Sniper: improved SNP discovery by multiply mapping deep sequenced reads Daniel F Simola, Junhyong Kim Genome Biology 2011, 12:R55 (20 June 2011) A method for improved SNP discovery in next-generation sequencing data
|
|
The characterisation of piRNA-related 19mers in the mouse Harald M Oey, Neil A Youngson, Emma Whitelaw BMC Genomics 2011, 12:315 (15 June 2011) |
|
CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping Tung Nguyen, Weisong Shi, Douglas Ruden BMC Research Notes 2011, 4:171 (6 June 2011) |
|
Microarrays, deep sequencing and the true measure of the transcriptome John H Malone, Brian Oliver BMC Biology 2011, 9:34 (31 May 2011) Global measures of gene expression can now be extracted either from microarrays or from RNA-seq, which do not always seem to give the same answer. Malone and Oliver review the advantages and limitations of each and conclude that, with some important exceptions, they tell the same story.
|
|
A novel and well-defined benchmarking method for second generation read mapping Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert BMC Bioinformatics 2011, 12:210 (26 May 2011) |
|
A high resolution map of a cyanobacterial transcriptome Vikram Vijayan, Isha H Jain, Erin K O'Shea Genome Biology 2011, 12:R47 (25 May 2011) A detailed transcriptome analysis of the cyanobacterium Synechococcus elongatus reveals widespread non coding transcription and transcript architecture
|
|
Enhancing genome assemblies by integrating non-sequence based data Thomas N Heider, James Lindsay, Chenwei Wang, Rachel J O’Neill, Andrew J Pask BMC Proceedings 2011, 5(Suppl 2):S7 (28 April 2011) |
|
Repeat-aware modeling and correction of short read errors Xiao Yang, Srinivas Aluru, Karin S Dorman BMC Bioinformatics 2011, 12(Suppl 1):S52 (15 February 2011) |
|
Sung-Joon Park, Kenta Nakai BMC Bioinformatics 2011, 12(Suppl 1):S50 (15 February 2011) |
|
UMARS: Un-MAppable Reads Solution Sung-Chou Li, Wen-Ching Chan, Chun-Hung Lai, Kuo-Wang Tsai, Chun-Nan Hsu, Yuh-Shan Jou, Hua-Chien Chen, Chun-Hong Chen, Wen-chang Lin BMC Bioinformatics 2011, 12(Suppl 1):S9 (15 February 2011) |
|
Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis Shaun Mahony, Esteban O Mazzoni, Scott McCuine, Richard A Young, Hynek Wichterle, David K Gifford Genome Biology 2011, 12:R2 (13 January 2011) ChIP-seq for retinoic acid receptor binding during early neuronal differentiation reveals a complex landscape of transcriptional control.
|
|
Galaxy CloudMan: delivering cloud compute clusters Enis Afgan, Dannon Baker, Nate Coraor, Brad Chapman, Anton Nekrutenko, James Taylor BMC Bioinformatics 2010, 11(Suppl 12):S4 (21 December 2010) |
|
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics Ronald C Taylor BMC Bioinformatics 2010, 11(Suppl 12):S1 (21 December 2010) |
|
NGSQC: cross-platform quality analysis pipeline for deep sequencing data Manhong Dai, Robert C Thompson, Christopher Maher, Rafael Contreras-Galindo, Mark H Kaplan, David M Markovitz, Gil Omenn, Fan Meng BMC Genomics 2010, 11(Suppl 4):S7 (2 December 2010) |
|
Quail Genomics: a knowledgebase for Northern bobwhite Arun Rawat, Kurt A Gust, Mohamed O Elasri, Edward J Perkins BMC Bioinformatics 2010, 11(Suppl 6):S13 (7 October 2010) |
|
The missing graphical user interface for genomics Michael C Schatz Genome Biology 2010, 11:128 (25 August 2010) The Galaxy package for genomic analysis empowers regular users through a much-needed and user-friendly graphical web interface.
|
|
Cloud-scale RNA-sequencing differential expression analysis with Myrna Ben Langmead, Kasper D Hansen, Jeffrey T Leek Genome Biology 2010, 11:R83 (11 August 2010) This article is part of a collection on Cloud computing tools and... Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
|
|
Leon Dent, Dana Marshall, Robert Hulette, Siddharth Pratap BMC Bioinformatics 2010, 11(Suppl 4):P16 (23 July 2010) |
|
C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris et al. Genome Biology 2010, 11:R73 (13 July 2010) The genome sequence of the plant pathogenic oomycete, Pythium ultimum and a comparison with the related potato blight pathogen genome reveals differences in pathogenicity.
|
|
Design and evaluation of genome-wide libraries for RNA interference screens Thomas Horn, Thomas Sandmann, Michael Boutros Genome Biology 2010, 11:R61 (15 June 2010) NEXT-RNAi allows the design and evaluation of genome-wide RNAi screens in any organism.
|
|
Effects of Alu elements on global nucleosome positioning in the human genome Yoshiaki Tanaka, Riu Yamashita, Yutaka Suzuki, Kenta Nakai BMC Genomics 2010, 11:309 (17 May 2010) |
|
BS Seeker: precise mapping for bisulfite sequencing Pao-Yang Chen, Shawn J Cokus, Matteo Pellegrini BMC Bioinformatics 2010, 11:203 (23 April 2010) |
|
James H Bullard, Elizabeth Purdom, Kasper D Hansen, Sandrine Dudoit BMC Bioinformatics 2010, 11:94 (18 February 2010) |
|
Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A Wilson, Dabing Zhang BMC Bioinformatics 2010, 11:81 (9 February 2010) |
|
Gene ontology analysis for RNA-seq: accounting for selection bias Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack Genome Biology 2010, 11:R14 (4 February 2010) GOseq is a method for GO analysis of RNA-seq data that takes into account the length bias inherent in RNA-seq |
|
Chunguang Liang, Alexander Schmid, María López-Sánchez, Andres Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar BMC Bioinformatics 2009, 10:391 (29 November 2009) |
|
Searching for SNPs with cloud computing Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009) This article is part of a collection on Cloud computing tools and... Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three. |
|
Simultaneous alignment of short reads against multiple genomes Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel Genome Biology 2009, 10:R98 (17 September 2009) New software for the alignment of short-read sequence data to multiple genomes allows identification of polymorphisms that cannot be identified by alignment to a single reference genome. |
|
Paul Flicek Genome Biology 2009, 10:212 (27 March 2009) A new sequence-alignment algorithm that uses advanced data structures to help data analysis keep pace with data generation. |