Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski, Alexey V Pyshkin, Alexander V Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A Alekseyev, Pavel A Pevzner. J Comput Biol 2012
Times Cited: 11415
Times Cited: 11415
Times Cited
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Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
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MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
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QUAST: quality assessment tool for genome assemblies.
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IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
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The RAST Server: rapid annotations using subsystems technology.
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Prodigal: prokaryotic gene recognition and translation initiation site identification.
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BLAST+: architecture and applications.
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
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In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.
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Identification of acquired antimicrobial resistance genes.
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The Sequence Alignment/Map format and SAMtools.
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Fast and sensitive protein alignment using DIAMOND.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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InterProScan 5: genome-scale protein function classification.
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NCBI prokaryotic genome annotation pipeline.
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PHASTER: a better, faster version of the PHAST phage search tool.
David Arndt, Jason R Grant, Ana Marcu, Tanvir Sajed, Allison Pon, Yongjie Liang, David S Wishart. Nucleic Acids Res 2016
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
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A large-scale evaluation of algorithms to calculate average nucleotide identity.
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun. Antonie Van Leeuwenhoek 2017
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Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.
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ModelFinder: fast model selection for accurate phylogenetic estimates.
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, Lars S Jermiin. Nat Methods 2017
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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
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ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes.
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MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
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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
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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
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
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antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.
Kai Blin, Simon Shaw, Katharina Steinke, Rasmus Villebro, Nadine Ziemert, Sang Yup Lee, Marnix H Medema, Tilmann Weber. Nucleic Acids Res 2019
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FastTree 2--approximately maximum-likelihood trees for large alignments.
Morgan N Price, Paramvir S Dehal, Adam P Arkin. PLoS One 2010
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Multilocus sequence typing of total-genome-sequenced bacteria.
Mette V Larsen, Salvatore Cosentino, Simon Rasmussen, Carsten Friis, Henrik Hasman, Rasmus Lykke Marvig, Lars Jelsbak, Thomas Sicheritz-Pontén, David W Ussery, Frank M Aarestrup,[...]. J Clin Microbiol 2012
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ResFinder 4.0 for predictions of phenotypes from genotypes.
Valeria Bortolaia, Rolf S Kaas, Etienne Ruppe, Marilyn C Roberts, Stefan Schwarz, Vincent Cattoir, Alain Philippon, Rosa L Allesoe, Ana Rita Rebelo, Alfred Ferrer Florensa,[...]. J Antimicrob Chemother 2020
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dbCAN2: a meta server for automated carbohydrate-active enzyme annotation.
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ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.
Dean Laslett, Bjorn Canback. Nucleic Acids Res 2004
Dean Laslett, Bjorn Canback. Nucleic Acids Res 2004
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Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Jan P Meier-Kolthoff, Alexander F Auch, Hans-Peter Klenk, Markus Göker. BMC Bioinformatics 2013
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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
Baofeng Jia, Amogelang R Raphenya, Brian Alcock, Nicholas Waglechner, Peiyao Guo, Kara K Tsang, Briony A Lago, Biren M Dave, Sheldon Pereira, Arjun N Sharma,[...]. Nucleic Acids Res 2017
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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.
Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks. Bioinformatics 2019
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Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
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GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.
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SignalP 5.0 improves signal peptide predictions using deep neural networks.
José Juan Almagro Armenteros, Konstantinos D Tsirigos, Casper Kaae Sønderby, Thomas Nordahl Petersen, Ole Winther, Søren Brunak, Gunnar von Heijne, Henrik Nielsen. Nat Biotechnol 2019
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progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.
Aaron E Darling, Bob Mau, Nicole T Perna. PLoS One 2010
Aaron E Darling, Bob Mau, Nicole T Perna. PLoS One 2010
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Easyfig: a genome comparison visualizer.
Mitchell J Sullivan, Nicola K Petty, Scott A Beatson. Bioinformatics 2011
Mitchell J Sullivan, Nicola K Petty, Scott A Beatson. Bioinformatics 2011
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