pypi: NanoPlot | Projects | Ecosyste.ms: Papers

10.1093/bioinformatics/bty149

NanoPack: visualizing and processing long-read sequencing data
Cited by: 1,423
Author(s): Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Software Mentions: 18
Published: over 6 years ago

10.12688/f1000research.51477.2

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
Cited by: 2
Author(s): Ann Mc Cartney, Medhat Mahmoud, Michael D. Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K. Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel Cameron, Joyjit Daw, Eric T. Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M. Khayat, Maximillian G. Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jimin Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Söylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin N. Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam C. English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J. Sedlazeck
Software Mentions: 14
Published: about 3 years ago

10.1186/s12915-021-01123-z

The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation
Cited by: 12
Author(s): Jana Sperschneider, Ashley Jones, Jamila Nasim, Bo Xu, Silke Jacques, Chengcheng Zhong, Narayana M. Upadhyaya, Rohit Mago, Yiheng Hu, Melania Figueroa, Karam B. Singh, Eric A. Stone, Ming-Bo Wang, Jennifer Taylor, Peter N. Dodds
Software Mentions: 9
Published: about 3 years ago

10.3389/fgene.2020.00211

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets
Cited by: 35
Author(s): Luca Cozzuto, Huanle Liu, Leszek P. Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Julia Ponomarenko, Eva María Novoa
Software Mentions: 6
Published: over 4 years ago

10.3389/fgene.2021.711437

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing
Cited by: 23
Author(s): Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer
Software Mentions: 5
Published: over 3 years ago

10.3390/genes11040445

MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples
Cited by: 25
Author(s): Adeline Seah, Marisa Lim, Denise McAloose, Stefan Prost, Tracie A. Seimon
Software Mentions: 5
Published: over 4 years ago

10.7717/peerj.11721

Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms
Cited by: 10
Author(s): Taylor Priest, Luis H. Orellana, Bruno Huettel, Bernhard M. Fuchs, Rudolf Amann
Software Mentions: 5
Published: over 3 years ago

10.1093/gigascience/giaa067

Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish
Cited by: 10
Author(s): Lisa K. Johnson, Ruta Sahasrabudhe, James Anthony Gill, Jennifer L. Roach, Lutz Froenicke, C. Titus Brown, Andrew Whitehead
Software Mentions: 4
Published: over 4 years ago

10.3390/genes11121444

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes
Cited by: 6
Author(s): Nazeefa Fatima, Anna Petri, Ulf Gyllensten, Lars Feuk, Adam Ameur
Software Mentions: 4
Published: almost 4 years ago

10.3390/v11121132

Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools
Cited by: 22
Author(s): Shaoyuan Tan, Cheryl M.T. Dvorak, Michael P. Murtaugh
Software Mentions: 4
Published: almost 5 years ago

10.1534/g3.120.401059

A Highly Contiguous Genome for the Golden-Fronted Woodpecker (Melanerpes aurifrons) via Hybrid Oxford Nanopore and Short Read Assembly
Cited by: 8
Author(s): Graham B. Wiley, Matthew J. Miller
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-021-07666-3

Re-examination of two diatom reference genomes using long-read sequencing
Cited by: 19
Author(s): Gina V. Filloramo, Bruce A. Curtis, Emma Blanche, John M. Archibald
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.42535

An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins
Cited by: 77
Author(s): Sergio A. Muñoz-Gómez, Sebastian Hess, Gertraud Burger, B. Franz Lang, Edward Susko, Claudio H. Slamovits, Andrew J. Roger
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000312

Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids
Cited by: 13
Author(s): Thomas Vognbjerg Sydenham, Søren Overballe‐Petersen, Henrik Hasman, Hannah M. Wexler, Michael Kemp, Ulrik Stenz Justesen
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-021-07767-z

MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction
Cited by: 20
Author(s): Valentine Murigneux, Leah W. Roberts, Brian M. Forde, Minh-Duy Phan, Nguyen Thi Khanh Nhu, Adam Irwin, Patrick N A Harris, David L. Paterson, Mark A. Schembri, David M. Whiley, Scott A. Beatson
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0253830

High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing
Cited by: 20
Author(s): Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin O. Borevitz, Benjamin Schwessinger
Software Mentions: 3
Published: over 3 years ago

10.1038/s41597-019-0311-3

Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta
Cited by: 21
Author(s): Robert Nowak, J Jastrzebski, Wiktor Kuśmirek, Rusłan Sałamatin, Małgorzata Rydzanicz, Agnieszka Sobczyk-Kopcioł, Anna Sulima-Celińska, Łukasz Paukszto, Karol G Makowczenko, Rafał Płoski, Vasyl V. Tkach, Katarzyna Basałaj, Daniel Młocicki
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0233170

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing
Cited by: 10
Author(s): William Taylor, John Pearson, Allison L. Miller, Sebastian Schmeier, Frank Frizelle, Rachel Purcell
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0235641

Genomic analyses of multidrug-resistant Salmonella Indiana, Typhimurium, and Enteritidis isolates using MinION and MiSeq sequencing technologies
Cited by: 14
Author(s): Chen Zhao, Dai Kuang, Xuebin Xu, Narjol González-Escalona, David L. Erickson, Eric W. Brown, Jianghong Meng
Software Mentions: 3
Published: over 4 years ago

10.1186/s13104-021-05484-0

Generating long-read sequences using Oxford Nanopore Technology from Diospyros celebica genomic DNA
Cited by: 3
Author(s): Iskandar Z. Siregar, Fifi Gus Dwiyanti, Rahadian Pratama, Deden Derajat Matra, Muhammad Majiidu
Software Mentions: 3
Published: over 3 years ago

10.3390/genes11121478

The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock
Cited by: 8
Author(s): Harrison J. Lamb, Ben J. Hayes, Loan Nguyen, Elizabeth M. Ross
Software Mentions: 3
Published: almost 4 years ago

10.1002/ece3.6151

Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification
Cited by: 18
Author(s): Nicolás D. Franco‐Sierra, Juan F. Díaz‐Nieto
Software Mentions: 3
Published: over 4 years ago

10.1093/g3journal/jkab211

Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex
Cited by: 2
Author(s): Sara J. Hanson, Eoin Ó Cinnéide, Letal I. Salzberg, Kenneth H. Wolfe, Jamie McGowan, David A. Fitzpatrick, Kate Matlin
Software Mentions: 3
Published: over 3 years ago

10.1007/s00253-021-11133-0

Complete genome sequence of lovastatin producer Aspergillus terreus ATCC 20542 and evaluation of genomic diversity among A. terreus strains
Cited by: 5
Author(s): Małgorzata Ryngajłło, Tomasz Boruta, Marcin Bizukojć
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2020.602313

Rapid and Detailed Characterization of Transgene Insertion Sites in Genetically Modified Plants via Nanopore Sequencing
Cited by: 7
Author(s): Paula Andrea Giraldo, Hiroshi Shinozuka, Germán Spangenberg, K. F. Smith, Noel O. I. Cogan
Software Mentions: 3
Published: almost 4 years ago

10.1093/femsle/fny069

Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies
Cited by: 15
Author(s): Ainsley Beaton, Cédric Lood, Edward Cunningham-Oakes, Alison Macfadyen, Alex J. Mullins, Walid E.l. Bestawy, João Botelho, Sylvie Chevalier, Shannon R. Coleman, Chloe Dalzell, Stephen K. Dolan, Alberto Faccenda, Maarten G. K. Ghequire, Steven A. Higgins, Alexander Kutschera, Jordan Murray, Martha L. Redway, Talal Sabhan Salih, Ana C. da Silva, Brian A. Smith, Nathan Smits, R. P.M. Thomson, Stuart Daniel Woodcock, Martin Welch, Pierre Cornélis, Rob Lavigne, Vera van Noort, Nicholas P. Tucker
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-28180-9

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus
Cited by: 57
Author(s): Sebastiaan Theuns, Bert Vanmechelen, Quinten Bernaert, Ward Deboutte, Marilou Vandenhole, Leen Beller, Jelle Matthijnssens, Piet Maes, Hans Nauwynck
Software Mentions: 2
Published: over 6 years ago

10.1186/s12866-020-01821-8

Nanopore sequencing reveals genomic map of CTX-M-type extended-spectrum β-lactamases carried by Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway
Cited by: 13
Author(s): Didrik H. Grevskott, Francisco Salvà‐Serra, Edward R. B. Moore, Nachiket P. Marathe
Software Mentions: 2
Published: over 4 years ago

10.1186/s12866-021-02225-y

WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates
Cited by: 1
Author(s): Astrid P. Heikema, Rick Jansen, Saskia Hiltemann, John P. Hays, Andrew Stubbs
Software Mentions: 2
Published: over 3 years ago

10.3390/md18090442

Nostoc edaphicum CCNP1411 from the Baltic Sea—A New Producer of Nostocyclopeptides
Cited by: 6
Author(s): Anna Fidor, Michał Grabski, Jan Gawor, Robert Gromadka, Grzegorz Węgrzyn, Hanna Mazur‐Marzec
Software Mentions: 2
Published: about 4 years ago

10.1128/MRA.01000-20

Telomere-to-Telomere Genome Assembly of Bursaphelenchus okinawaensis Strain SH1
Cited by: 6
Author(s): Simo Sun, Ryoji Shinya, Mehmet Dayı, Akemi Yoshida, Paul W. Sternberg, Taisei Kikuchi
Software Mentions: 2
Published: about 4 years ago

10.1128/MRA.01233-20

Complete Genome Sequence of Francisella sp. Strain LA11-2445 (FDC406), a Novel Francisella Species Isolated from a Human Skin Lesion
Cited by: 0
Author(s): Caroline Öhrman, Ingrid Uneklint, Linda Karlsson, Laurel B. Respicio-Kingry, Mats Forsman, Jeannine M. Petersen, Andreas Sjödin
Software Mentions: 2
Published: almost 4 years ago

10.1128/MRA.00021-19

Complete Genome Sequence of Caldicellulosiruptor changbaiensis CBS-Z, an Extremely Thermophilic, Cellulolytic Bacterium Isolated from a Hot Spring in China
Cited by: 4
Author(s): Carl Mendoza, Sara E. Blumer-Schuette
Software Mentions: 2
Published: over 5 years ago

10.1128/MRA.01213-20

Genome Sequence of the Fungus Nannizziopsis barbatae, an Emerging Reptile Pathogen
Cited by: 1
Author(s): Daniel Powell, Ashley Jones, Nicola Kent, Parwinder Kaur, Ido Bar, Benjamin Schwessinger, Céline Frère
Software Mentions: 2
Published: almost 4 years ago

10.1128/MRA.00055-20

Complete Genome Sequence of Pseudomonas putida Strain TS312, Harboring an HdtS-Type N -Acyl-Homoserine Lactone Synthase, Isolated from a Paper Mill
Cited by: 2
Author(s): Ayaka Hosoe, Toshikazu Suenaga, Takumi Sugi, Taro Iizumi, Naohiro Nagai, Akihiko Terada
Software Mentions: 2
Published: over 4 years ago

10.1128/MRA.01257-20

Whole-Genome Shotgun Sequence of Bacillus mycoides Strain U53, a Psychrotolerant Bacterium Isolated from the Sakhalin Region in Russia
Cited by: 1
Author(s): Ha My T. Phan, М. Л. Сидоренко, Po Chun Tsai, Shir Ly Huang
Software Mentions: 2
Published: almost 4 years ago

10.3390/microorganisms9050903

Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
Cited by: 17
Author(s): Sélim Ben Chéhida, Denis Filloux, Emmanuel Fernandez, Oumaima Moubset, Murielle Hoareau, Charlotte Julian, Laurence Blondin, Jean‐Michel Lett, Denis Filloux, Pierre Lefeuvre
Software Mentions: 2
Published: over 3 years ago

10.3390/pathogens10091183

Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents
Cited by: 7
Author(s): Nusrat Jahan, Laramie L. Lindsey, Evan J. Kipp, Adam Reinschmidt, Brad Heins, Amy M. Runck, Peter A. Larsen
Software Mentions: 2
Published: about 3 years ago

10.7717/peerj.10778

Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis
Cited by: 13
Author(s): Liying Low, Pablo Fuentes-Utrilla, James Hodson, John D. O’Neil, Amanda E. Rossiter, Ghazala Begum, Kusy Suleiman, Philip I. Murray, Graham R. Wallace, Nicholas J. Loman, Saaeha Rauz
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0219961

Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing
Cited by: 8
Author(s): Taylor Sheahan, Rhys Hakstol, Senthilkumar Kailasam, Graeme D. Glaister, Andrew J. Hudson, Hans-Joachim Wieden
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2020.00011

Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer
Cited by: 9
Author(s): K. Imai, Rina Nemoto, Masahiro Kodana, Norihito Tarumoto, Jun Sakai, Tomohiro Kawamura, Kenji Ikebuchi, Kotaro Mitsutake, Takashi Murakami, Shigefumi Maesaki, Taku Fujiwara, Satoshi Hayakawa, T. Hoshino, Mitsuko Seki, Takeshi Maeda
Software Mentions: 2
Published: almost 5 years ago

10.3389/fimmu.2020.582927

Efficient Sequencing, Assembly, and Annotation of Human KIR Haplotypes
Cited by: 8
Author(s): David Roe, Jonathan Williams, Keyton Ivery, Jenny Brouckaert, Nick Downey, Chad Locklear, Rui Kuang, Martin Maiers
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2021.637771

Evaluation of Salmonella Serotype Prediction With Multiplex Nanopore Sequencing
Cited by: 5
Author(s): Xinqi Wu, Hao Luo, Feng Xu, Chongtao Ge, Shaoting Li, Xiangyu Deng, Martin Wiedmann, R. C. Baker, Abigail E. Stevenson, Guangtao Zhang, Silin Tang
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.515319

Genomic and Functional Characterization of Enterococcus faecalis Isolates Recovered From the International Space Station and Their Potential for Pathogenicity
Cited by: 9
Author(s): Noelle C. Bryan, François Lebreton, Michael S. Gilmore, Gary Ruvkun, M. T. Zuber, Christopher E. Carr
Software Mentions: 2
Published: almost 4 years ago

10.1093/gigascience/giaa037

The gene-rich genome of the scallop Pecten maximus
Cited by: 46
Author(s): Nathan J. Kenny, Shane McCarthy, Olga Dudchenko, Katherine James, Emma Betteridge, Craig Corton, Jale Dolucan, Daniel Mead, Karen Oliver, Arina D. Omer, Sarah Pelan, Yan Ryan, Ying Sims, Jason Skelton, Michelle Smith, James Torrance, David Weisz, Anil Wipat, E Aiden, Kerstin Howe, Suzanne T. Williams
Software Mentions: 2
Published: over 4 years ago

10.1093/gigascience/giaa146

Comparison of long-read methods for sequencing and assembly of a plant genome
Cited by: 61
Author(s): Valentine Murigneux, Subash Kumar, Agnelo Furtado, Timothy J. C. Bruxner, Wei Tian, Ivon Harliwong, Hanmin Wei, Bicheng Yang, Qianyu Ye, Ellis Anderson, Qing Mao, Radoje Drmanac, Ou Wang, Brock A. Peters, Mengyang Xu, Pei‐Ju Wu, Bruce Topp, Lachlan Coin, Robert J. Henry
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-019-55908-y

De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell
Cited by: 5
Author(s): Joseph R. Fauver, John Martin, Gary J. Weil, Makedonka Mitreva, Peter Fischer
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-61989-x

Benchmarking the MinION: Evaluating long reads for microbial profiling
Cited by: 26
Author(s): Robert Maximilian Leidenfrost, Dierk-Christoph Pöther, Udo Jäckel, Röbbe Wünschiers
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-68249-y

Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies
Cited by: 2
Author(s): Francisco Salvà‐Serra, Daniel Jaén‐Luchoro, Hedvig E. Jakobsson, Lucia Gonzales-Silès, Roger Karlsson, Antonio Busquets, Margarita Gomila, Antonio Bennasar, Julie E. Russell, Mohammed Abbas Fazal, Sarah Alexander, Edward R. B. Moore
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-94820-2

Transcriptomics differentiate two novel bioactive strains of Paenibacillus sp. isolated from the perennial ryegrass seed microbiome
Cited by: 5
Author(s): Tongda Li, Ross Mann, Jatinder Kaur, Germán Spangenberg, Tim Sawbridge
Software Mentions: 2
Published: over 3 years ago

10.1128/mBio.00532-20

RhlR-Regulated Acyl-Homoserine Lactone Quorum Sensing in a Cystic Fibrosis Isolate of Pseudomonas aeruginosa
Cited by: 52
Author(s): Renae L. Cruz, Kyle L. Asfahl, Sara Van den Bossche, Tom Coenye, Aurélie Crabbé, Ajai A. Dandekar
Software Mentions: 2
Published: over 4 years ago

10.1128/mSystems.00083-21

Limited and Strain-Specific Transcriptional and Growth Responses to Acquisition of a Multidrug Resistance Plasmid in Genetically Diverse Escherichia coli Lineages
Cited by: 19
Author(s): Steven Dunn, Laura Carrilero, Michael A. Brockhurst, Alan McNally
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22084144

Antarctic Rahnella inusitata: A Producer of Cold-Stable β-Galactosidase Enzymes
Cited by: 7
Author(s): Kattia Núñez-Montero, Rodrigo Salazar, Andrés Santos, Olman Gómez-Espinoza, Scandar Farah, Claudia Troncoso, Catalina Hoffmann, Damaris Melivilu, Felipe Scott, Leticia Barrientos
Software Mentions: 2
Published: over 3 years ago

10.1128/MRA.00680-21

Complete Genome Sequence of Caulobacter sp. Strain S6, Obtained Using Oxford Nanopore and Illumina Sequencing
Cited by: 0
Author(s): Cuiyang Zhang, Jun Huang, Wei Ouyang, Yongmei Li, Ying Tang, Zhaohui Guo, Ping Lei, Qingshu Liu
Software Mentions: 1
Published: about 3 years ago

10.1128/MRA.00996-20

Metagenome of a Bronchoalveolar Lavage Fluid Sample from a Confirmed COVID-19 Case in Quito, Ecuador, Obtained Using Oxford Nanopore MinION Technology
Cited by: 0
Author(s): Sully Márquez, Belén Prado-Vivar, Juan José Guadalupe, Bernardo Gutiérrez, Mónica Becerra-Wong, Manuel Jibaja, Milton Tobar, Verónica Barragán, Patricio Rojas-Silva, Joséfina Coloma, Gabriel Trueba, Michelle Grunauer, Paúl Cárdenas
Software Mentions: 1
Published: about 4 years ago

10.1186/s12866-021-02094-5

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution
Cited by: 108
Author(s): Yoshiyuki Matsuo, Shinnosuke Komiya, Yoshiaki Yasumizu, Yuki Yasuoka, Katsura Mizushima, Tomohisa Takagi, Kirill Kryukov, Aisaku Fukuda, Yoshiharu Morimoto, Yuji Naito, Hidetaka Okada, Hidemasa Bono, So Nakagawa, Kiichi Hirota
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00299-21

High-Quality Genome Reconstruction of Candida albicans CHN1 Using Nanopore and Illumina Sequencing and Hybrid Assembly
Cited by: 3
Author(s): Shipra Garg, Piyush Ranjan, John R. Erb-Downward, Gary B. Huffnagle
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.01335-20

Complete Genome Sequence of Exfoliative Toxin-Producing Staphylococcus aureus Strain MSSA_SSSS_01, Obtained from a Case of Staphylococcal Scalded-Skin Syndrome
Cited by: 2
Author(s): Eleonora Cella, Michael Z. David, Mohammad Jubair, Sarah L. Baines, David A. Pegues, Taj Azarian
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12879-020-05367-y

Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses
Cited by: 29
Author(s): Jacqueline King, Timm Harder, Martin Beer, Anne Pohlmann
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2020.580960

Characterization of IncC Plasmids in Enterobacterales of Food-Producing Animals Originating From China
Cited by: 5
Author(s): Yu Zhang, Changwei Lei, Xuan Chen, Tian-Ge Yao, Jingwen Yu, Wan-Long Hu, Xuan Mao
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2020.01991

Novel Xanthomonas Species From the Perennial Ryegrass Seed Microbiome – Assessing the Bioprotection Activity of Non-pathogenic Relatives of Pathogens
Cited by: 16
Author(s): Tongda Li, Ross Mann, Tim Sawbridge, Jatinder Kaur, Desmond Auer, Germán Spangenberg
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-018-37497-4

Diagnosis and characterization of canine distemper virus through sequencing by MinION nanopore technology
Cited by: 21
Author(s): Alessia Peserico, Maurilia Marcacci, Daniela Malatesta, Marco Di Domenico, Annamaria Pratelli, Iolanda Mangone, Nicola D’Alterio, Federica Pizzurro, Francesco Cirone, Guendalina Zaccaria, Cesare Cammà, Alessio Lorusso
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-74180-z

Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION
Cited by: 45
Author(s): Keren Davidov, Evgenia Iankelevich-Kounio, Iryna Yakovenko, Yuri Koucherov, Maxim Rubin‐Blum, Matan Oren
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2020.619423

Biocontrol Using Bacillus amyloliquefaciens PP19 Against Litchi Downy Blight Caused by Peronophythora litchii
Cited by: 4
Author(s): Li Zheng, Shilian Huang, Tom Hsiang, Yu Gui, Dongliang Guo, Zide Jiang, Jianguang Li
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00113-20

Complete Genome Sequence of Methylosinus sp. Strain C49, a Methane-Oxidizing Bacterium Harboring phaABC Genes for Polyhydroxyalkanoate Synthesis
Cited by: 0
Author(s): Shohei Yasuda, Toshikazu Suenaga, Akihiko Terada
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2021.656049

Targeted Enrichment of rRNA Gene Tandem Arrays for Ultra-Long Sequencing by Selective Restriction Endonuclease Digestion
Cited by: 4
Author(s): Anastasia McKinlay, Dalen Fultz, Zhen Wang, Craig S. Pikaard
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00203-21

Complete Genome Sequence of Chlamydia abortus MRI-10/19, Isolated from a Sheep Vaccinated with the Commercial Live C. abortus 1B Vaccine Strain
Cited by: 2
Author(s): Morag Livingstone, Sergio Gastón Caspe, David Longbottom
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00176-20

Draft Genome Sequence of Verrucosispora sp. Strain CWR15, Isolated from a Gulf of Mexico Sponge
Cited by: 2
Author(s): S. Kennedy, Eleonora Cella, Mohammad Jubair, Taj Azarian, Bill J. Baker, Lindsey N. Shaw
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.01002-20

Nearly Complete Genome Assembly of the Pinewood Nematode Bursaphelenchus xylophilus Strain Ka4C1
Cited by: 9
Author(s): Mehmet Dayı, Simo Sun, Y. Maeda, Ryusei Tanaka, Akemi Yoshida, Isheng Jason Tsai, Taisei Kikuchi
Software Mentions: 1
Published: about 4 years ago

10.1128/MRA.01415-20

Complete Genome Sequence of Sandaracinobacter sp. Strain M6, Isolated from a Rocky Mountain in China
Cited by: 0
Author(s): Ying Tang, Jun Huang, Cuiyang Zhang, Shiyu Bi, Zhaohui Guo, Qingshu Liu, Ping Lei
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13068-018-1258-x

Genetic repertoires of anaerobic microbiomes driving generation of biogas
Cited by: 5
Author(s): Anja Grohmann, Yevhen Vainshtein, Ellen Euchner, Christian Grumaz, Dieter Bryniok, Ralf Rabus, Kai Sohn
Software Mentions: 1
Published: about 6 years ago

10.1093/gbe/evaa048

Genome Sequence of an Emerging Salmonella enterica Serovar Infantis and Genomic Comparison with Other S. Infantis Strains
Cited by: 18
Author(s): Emiliano Cohen, Galia Rahav, Ohad Gal-Mor
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.00463-20

Draft Genome Sequence of the Bacterium Paraburkholderia aromaticivorans AR20-38, a Gram-Negative, Cold-Adapted Degrader of Aromatic Compounds
Cited by: 5
Author(s): Caroline Poyntner, De-Chao Zhang, Rosa Margesin
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.01078-20

De Novo Whole-Genome Sequencing and Annotation of Pathogenic Bovine Pasteurella multocida Type A:3 Strains
Cited by: 1
Author(s): Morag Livingstone, Kevin Aitchison, Mark P. Dagleish, David Longbottom
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00222-21

Complete Genome Sequence of a Pseudomonas simiae Strain with Biocontrol Potential against Aphanomyces Root Rot
Cited by: 0
Author(s): Ashebir T. Godebo, Keith D. MacKenzie, F.L. Walley, James J. Germida, Christopher K. Yost
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms22147668

Comparison of De Novo Assembly Strategies for Bacterial Genomes
Cited by: 16
Author(s): Pengfei Zhang, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, Zexiao Yang
Software Mentions: 1
Published: over 3 years ago

10.3390/microorganisms8050763

Evaluation of a Highly Efficient DNA Extraction Method for Bacillus anthracis Endospores
Cited by: 14
Author(s): Mandy Knüpfer, Peter Braun, Karl Baumann, Alexandra Rehn, Markus Antwerpen, Gregor Grass, Roman Wölfel
Software Mentions: 1
Published: over 4 years ago

10.1186/s13104-021-05457-3

Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing
Cited by: 6
Author(s): Michael Liem, Tonny Regensburg-Tuïnk, Christiaan V. Henkel, Hans J. Jansen, Herman P. Spaink
Software Mentions: 1
Published: almost 4 years ago

10.3390/vaccines9030237

Complete Genome Sequence, Genome Stability and Phylogeny of the Vaccine Strain Mycobacterium bovis BCG SL222 Sofia
Cited by: 6
Author(s): Stefan Panaiotov, Yordan Hodzhev, Vladimir Tolchkov, Borislava Tsafarova, Alexander Mihailov, Tzvetelina Stefanova
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00414-20

Draft Genome Assembly of Rhodobacter sphaeroides 2.4.1 Substrain H2 from Nanopore Data
Cited by: 2
Author(s): Robert Maximilian Leidenfrost, Nadine Wappler, Röbbe Wünschiers
Software Mentions: 1
Published: over 4 years ago

10.3390/v12101136

Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model
Cited by: 3
Author(s): Shaoyuan Tan, Cheryl M.T. Dvorak, Michael P. Murtaugh
Software Mentions: 1
Published: about 4 years ago

10.1093/gigascience/giaa105

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
Cited by: 21
Author(s): Willem de Koning, Milad Miladi, Saskia Hiltemann, Astrid P. Heikema, John P. Hays, Stephan Flemming, Marius van den Beek, Dana A. M. Mustafa, Rolf Backofen, Björn Grüning, Andrew Stubbs
Software Mentions: 1
Published: about 4 years ago

10.1186/s12863-021-00969-0

De novo genome assembly and analysis unveil biosynthetic and metabolic potentials of Pseudomonas fragi A13BB
Cited by: 3
Author(s): Opeyemi K. Awolope, Noëlle H. O’Driscoll, Alberto Di Salvo, Andrew J. Lamb
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.01190-20

Complete Genome Sequences of 12 Quinolone-Resistant Escherichia coli Strains Containing qnrS1 Based on Hybrid Assemblies
Cited by: 1
Author(s): Håkon Kaspersen, Thomas Haverkamp, Hanna Karin Ilag, Øivind Øines, Camilla Sekse, Jannice Schau Slettemeås
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00627-21

Complete Genome Sequence of Atopobiaceae Bacterium Strain P1, Isolated from Mouse Feces
Cited by: 1
Author(s): Yasuha Watanabe, Naonobu Takeuchi, Jiayue Yang, Nozomu Obana, Kana Morinaga, Hiroyuki Kusada, Hideyuki Tamaki, Shinji Fukuda, Kazuharu Arakawa
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00634-21

Complete Genome Sequence of Lactobacillus crispatus Type Strain ATCC 33820
Cited by: 2
Author(s): Lucia Teodori, Lorenzo Colombini, Anna Maria Cuppone, Elisa Lazzeri, David Pinzauti, Francesco Santoro, Francesco Iannelli, Gianni Pozzi
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00134-21

Complete Multipartite Genome Sequence of the Cupriavidus basilensis Type Strain, a 2,6-Dichlorophenol-Degrading Bacterium
Cited by: 4
Author(s): Francisco Salvà‐Serra, Raúl Donoso, Kyoung Hee Cho, Ji A. Yoo, Kihyun Lee, Seok-Hwan Yoon, Beatriz Piñeiro-Iglesias, Edward R. B. Moore, Danilo Pérez‐Pantoja
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.ppat.1009451

Pathoadaptation of the passerine-associated Salmonella enterica serovar Typhimurium lineage to the avian host
Cited by: 19
Author(s): Emiliano Cohen, Shalevet Azriel, Oren Auster, Adiv Gal, Carmel Zitronblat, Svetlana Mikhlin, Felix Scharte, Michael Hensel, Galia Rahav, Ohad Gal-Mor
Software Mentions: 1
Published: over 3 years ago

10.1186/s13578-021-00566-9

When the genome bluffs: a tandem duplication event during generation of a novel Agmo knockout mouse model fools routine genotyping
Cited by: 11
Author(s): S Sailer, Stefan Coassin, Katharina Lackner, Caroline Fischer, Eileen McNeill, Gertraud Streiter, Christian Kremser, Manuel Maglione, Catherine Green, Daniela Moralli, Alexander R. Moschen, Markus A. Keller, Georg Golderer, Gabriele Werner-Felmayer, Irmgard Tegeder, Keith M. Channon, Benjamin M Davies, Ernst R. Werner, Katrin Watschinger
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.01079-20

Complete Genome Sequence of an Australian Strain of the Lichen-Forming Fungus Endocarpon pusillum (Hedwig)
Cited by: 4
Author(s): Oliver Mead, Cécile Gueidan
Software Mentions: 1
Published: almost 4 years ago

Projects: pypi: NanoPlot

Papers Mentioning NanoPlot 90