Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Grant R Cramer, Massimo Delledonne, Chongyuan Luo, Joseph R Ecker, Dario Cantu, David R Rank, Michael C Schatz. Nat Methods 2016
Times Cited: 919
Times Cited: 919
Times Cited
Times Co-cited
Similarity
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
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Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
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The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman. Genome Biol 2008
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman. Genome Biol 2008
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A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Guillaume Marçais, Carl Kingsford. Bioinformatics 2011
Guillaume Marçais, Carl Kingsford. Bioinformatics 2011
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Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
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LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.
Zhao Xu, Hao Wang. Nucleic Acids Res 2007
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OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li Li, Christian J Stoeckert, David S Roos. Genome Res 2003
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Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
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MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
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Infernal 1.1: 100-fold faster RNA homology searches.
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Using RepeatMasker to identify repetitive elements in genomic sequences.
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Full-length transcriptome assembly from RNA-Seq data without a reference genome.
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CAFE: a computational tool for the study of gene family evolution.
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De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
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HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
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OrthoFinder: phylogenetic orthology inference for comparative genomics.
David M Emms, Steven Kelly. Genome Biol 2019
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MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
Kazutaka Katoh, Daron M Standley. Mol Biol Evol 2013
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Basic local alignment search tool.
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tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
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De novo assembly of haplotype-resolved genomes with trio binning.
Sergey Koren, Arang Rhie, Brian P Walenz, Alexander T Dilthey, Derek M Bickhart, Sarah B Kingan, Stefan Hiendleder, John L Williams, Timothy P L Smith, Adam M Phillippy. Nat Biotechnol 2018
Sergey Koren, Arang Rhie, Brian P Walenz, Alexander T Dilthey, Derek M Bickhart, Sarah B Kingan, Stefan Hiendleder, John L Williams, Timothy P L Smith, Adam M Phillippy. Nat Biotechnol 2018
13
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies.
Michael J Roach, Simon A Schmidt, Anthony R Borneman. BMC Bioinformatics 2018
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RepeatModeler2 for automated genomic discovery of transposable element families.
Jullien M Flynn, Robert Hubley, Clément Goubert, Jeb Rosen, Andrew G Clark, Cédric Feschotte, Arian F Smit. Proc Natl Acad Sci U S A 2020
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GenomeScope: fast reference-free genome profiling from short reads.
Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, Charles J Underwood, Han Fang, James Gurtowski, Michael C Schatz. Bioinformatics 2017
Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, Charles J Underwood, Han Fang, James Gurtowski, Michael C Schatz. Bioinformatics 2017
13
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
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TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
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De novo identification of repeat families in large genomes.
Alkes L Price, Neil C Jones, Pavel A Pevzner. Bioinformatics 2005
Alkes L Price, Neil C Jones, Pavel A Pevzner. Bioinformatics 2005
13
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Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Joshua N Burton, Andrew Adey, Rupali P Patwardhan, Ruolan Qiu, Jacob O Kitzman, Jay Shendure. Nat Biotechnol 2013
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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li. Nat Methods 2021
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li. Nat Methods 2021
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MUMmer4: A fast and versatile genome alignment system.
Guillaume Marçais, Arthur L Delcher, Adam M Phillippy, Rachel Coston, Steven L Salzberg, Aleksey Zimin. PLoS Comput Biol 2018
Guillaume Marçais, Arthur L Delcher, Adam M Phillippy, Rachel Coston, Steven L Salzberg, Aleksey Zimin. PLoS Comput Biol 2018
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MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Robert C Edgar. Nucleic Acids Res 2004
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Repbase Update, a database of repetitive elements in eukaryotic genomes.
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fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
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RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Staerfeldt, Torbjørn Rognes, David W Ussery. Nucleic Acids Res 2007
Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Staerfeldt, Torbjørn Rognes, David W Ussery. Nucleic Acids Res 2007
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Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
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GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.
T Rhyker Ranallo-Benavidez, Kamil S Jaron, Michael C Schatz. Nat Commun 2020
T Rhyker Ranallo-Benavidez, Kamil S Jaron, Michael C Schatz. Nat Commun 2020
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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.
Neva C Durand, Muhammad S Shamim, Ido Machol, Suhas S P Rao, Miriam H Huntley, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016
Neva C Durand, Muhammad S Shamim, Ido Machol, Suhas S P Rao, Miriam H Huntley, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016
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Synteny and collinearity in plant genomes.
Haibao Tang, John E Bowers, Xiyin Wang, Ray Ming, Maqsudul Alam, Andrew H Paterson. Science 2008
Haibao Tang, John E Bowers, Xiyin Wang, Ray Ming, Maqsudul Alam, Andrew H Paterson. Science 2008
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CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
Genis Parra, Keith Bradnam, Ian Korf. Bioinformatics 2007
Genis Parra, Keith Bradnam, Ian Korf. Bioinformatics 2007
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LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons.
David Ellinghaus, Stefan Kurtz, Ute Willhoeft. BMC Bioinformatics 2008
David Ellinghaus, Stefan Kurtz, Ute Willhoeft. BMC Bioinformatics 2008
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Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
11
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.