Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
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12,661 citations
Cites background from "Aligning sequence reads, clone sequ..."
...…Leader), David M. Altshuler3, Eric Banks13, Gaurav Bhatia13, Guillermo del Angel13, Stacey B. Gabriel13, Giulio Genovese13, Namrata Gupta13, Heng Li13, Seva Kashin13,40, Eric S. Lander13, Steven A. McCarroll13,40, James C. Nemesh13, Ryan E. Poplin13; Cold Spring Harbor Laboratory Seungtai C.…...
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...…Robert E. Handsaker13,40 (Project Leader), David M. Altshuler3, Eric Banks13, Guillermo del Angel13, Giulio Genovese13, Chris Hartl13, Heng Li13, Seva Kashin13,40, James C. Nemesh13, Khalid Shakir13; Cold Spring Harbor Laboratory Seungtai C. Yoon42 (Principal Investigator), Jayon…...
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...Garrison4 (Project Lead),Deniz Kural37,Wan-PingLee37, Wen Fung Leong38, Michael Stromberg39, Alistair N. Ward23, Jiantao Wu39, Mengyao Zhang40; Broad Institute of MIT and Harvard Mark J. Daly13 (Principal Investigator), Mark A. DePristo41 (Project Leader), Robert E. Handsaker13,40 (Project Leader), David M. Altshuler3, Eric Banks13, Gaurav Bhatia13, Guillermo del Angel13, Stacey B. Gabriel13, Giulio Genovese13, Namrata Gupta13, Heng Li13, Seva Kashin13,40, Eric S. Lander13, Steven A. McCarroll13,40, James C. Nemesh13, Ryan E. Poplin13; Cold Spring Harbor Laboratory Seungtai C. Yoon42 (Principal Investigator), Jayon Lihm42, Vladimir Makarov43; Cornell University Andrew G. Clark7 (Principal Investigator), Srikanth Gottipati44, Alon Keinan7, Juan L. Rodriguez-Flores45; European Molecular Biology Laboratory Jan O. Korbel12,17 (Principal Investigator), Tobias Rausch17,46 (Project Leader),Markus H. Fritz46, Adrian M. 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Kidd91,92 (Principal Investigator), Tom Blackwell2, Sean Caron2, Wei Chen93, Sarah Emery92, Lars Fritsche2, Christian Fuchsberger2, Goo Jun2,94, Bingshan Li95, Robert Lyons96, Chris Scheller2, Carlo Sidore2,97,98, Shiya Song91, Elzbieta Sliwerska92, Daniel Taliun2, Adrian Tan2, Ryan Welch2, Mary Kate Wing2, Xiaowei Zhan99; University of Montréal Philip Awadalla62,100 (Principal Investigator), Alan Hodgkinson100; University of North Carolina at Chapel Hill Yun Li101; University of North Carolina at Charlotte Xinghua Shi102 (Principal Investigator), Andrew Quitadamo102; University of Oxford Gerton Lunter8 (Principal Investigator), Gil A. McVean8,9 (Principal Investigator) (Co-Chair), Jonathan L. Marchini8,9 (Principal Investigator), Simon Myers8,9 (Principal Investigator), Claire Churchhouse9, Olivier Delaneau9,87, Anjali Gupta-Hinch8, Warren Kretzschmar8, Zamin Iqbal8, Iain Mathieson8, Androniki Menelaou9,103, Andy Rimmer87, Dionysia K. Xifara8,9; University of Puerto Rico Taras K. 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Yoon42 (Principal Investigator), Jayon Lihm42, Vladimir Makarov43; Cornell University Jeremiah Degenhardt7; European Molecular Biology Laboratory Jan O. Korbel12,17 (Principal Investigator) (Co-Chair), Markus H. Fritz46, Sascha Meiers17, Benjamin Raeder17, Tobias Rausch17,46, Adrian M. Stütz17; European Molecular Biology Laboratory, European Bioinformatics Institute Paul Flicek12 (Principal Investigator), Francesco Paolo Casale12, Laura Clarke12, Richard E. Smith12, Oliver Stegle12, Xiangqun Zheng-Bradley12; Illumina David R. Bentley5 (Principal Investigator), Bret Barnes39, R. Keira Cheetham5, Michael Eberle5, Sean Humphray5, Scott Kahn39, Lisa Murray5, Richard Shaw5; Leiden University Medical Center Eric-Wubbo Lameijer118; Louisiana State University Mark A. Batzer52 (Principal Investigator), Miriam K. Konkel52, Jerilyn A. Walker52; McDonnell Genome Institute at Washington University Li Ding22 (Principal Investigator), Ira Hall22, Kai Ye22; Stanford University Phil Lacroute65; The Jackson Laboratory for Genomic Medicine Charles Lee18,19 (Principal Investigator) (Co-Chair), Eliza Cerveira18, Ankit Malhotra18, Jaeho Hwang18, Dariusz Plewczynski18, Kamen Radew18, Mallory Romanovitch18, Chengsheng Zhang18; Translational Genomics Research Institute David W. Craig74 (Principal Investigator), Nils Homer75; US National Institutes of Health Deanna Church34, Chunlin Xiao25; University of California,San Diego JonathanSebat77 (Principal Investigator),Danny Antaki77, Vineet Bafna119, Jacob Michaelson120, Kenny Ye79; University of Maryland School of Medicine Scott E. Devine90 (Principal Investigator), Eugene J. Gardner90 (Project Leader); University of Michigan Gonçalo R. Abecasis2 (Principal Investigator), Jeffrey M. Kidd91,92 (Principal Investigator), Ryan E. Mills91,92 (Principal Investigator), Gargi G2015 Macmillan Publishers Limited....
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6,264 citations
Cites background or methods from "Aligning sequence reads, clone sequ..."
...Several aligners have been developed for such data (Chaisson and Tesler, 2012; Li, 2013; Liu et al., 2016; Sović et al., 2016; Liu et al., 2017; Lin and Hsu, 2017; Sedlazeck et al., 2017)....
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...) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length at an error rate ˘15%. Several aligners have been developed for such data (Chaisson and Tesler, 2012; Li, 2013; Liu et al., 2016; Sovic et al., 2016; Liu et al., 2017; Lin and Hsu, 2017; Sedlazeck´ et al., 2017). Most of them were five times as slow as mainstream short-read aligners (Langmead and Salzberg, 201...
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...7.15; Li, 2013), GraphMap (v0....
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...Most of them were five times as slow as mainstream short-read aligners (Langmead and Salzberg, 2012; Li, 2013) in terms of the number of bases mapped per second....
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...ses such as nt from NCBI. 3.1 Aligning long genomic reads As a sanity check, we evaluated minimap2 on simulated human reads along with BLASR (v1.MC.rc64; Chaisson and Tesler, 2012), BWA-MEM (v0.7.15; Li, 2013), GraphMap (v0.5.2; Sovic et al.,´ 2016), Kart (v2.2.5; Lin and Hsu, 2017), minialign (v0.5.3; https://github.com/ocxtal/minialign) and NGMLR (v0.2.5; Sedlazeck et al., 2017). We excluded rHAT (Liu et...
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4,855 citations
2,245 citations
1,820 citations
References
70,111 citations
43,862 citations
"Aligning sequence reads, clone sequ..." refers background in this paper
...2.2.1 Rescuing missing hitsLike BWA (Li and Durbin, 2009), BWAMEM processes a batch of reads at a time....
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37,898 citations
"Aligning sequence reads, clone sequ..." refers methods in this paper
...Bowtie2 and Cushaw2 are slower for 600bp reads (see Results)....
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...In this background, a few long-read alignment algorithms, notably including BWA-SW (Li and Durbin, 2010), Bowtie2 (Langmead and Salzberg, 2012), Cushaw2 (Liu and Schmidt, 2012) and GEM (Marco-Sola et al., 2012), have been developed....
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...On speed, BWA-MEM is similar to GEM and Bowtie2 for this data set, but is about 6 times as fast as Bowtie2 and Cushaw2 for a 650bp long-read data set....
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...We evaluated the performance of BWA-MEM on simulated data together with NovoAlign (http://novocraft.com), GEM, Bowtie2, Cushaw2, SeqAlto (Mu et al., 2012), BWA-SW and BWA (Figure 1)....
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4,886 citations