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ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes
Florensa, Alfred Ferrer, Kaas, Rolf Sommer, Clausen, Philip Thomas Lanken Conradsen, Aytan-Aktug, Derya, Aarestrup, Frank M.
Published in Microbial genomics (01.01.2022)
Published in Microbial genomics (01.01.2022)
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Completing bacterial genome assemblies with multiplex MinION sequencing
Wick, Ryan R., Judd, Louise M., Gorrie, Claire L., Holt, Kathryn E.
Published in Microbial genomics (01.10.2017)
Published in Microbial genomics (01.10.2017)
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SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
Page, Andrew J., Taylor, Ben, Delaney, Aidan J., Soares, Jorge, Seemann, Torsten, Keane, Jacqueline A., Harris, Simon R.
Published in Microbial genomics (01.04.2016)
Published in Microbial genomics (01.04.2016)
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ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Hunt, Martin, Mather, Alison E, Sánchez-Busó, Leonor, Page, Andrew J, Parkhill, Julian, Keane, Jacqueline A, Harris, Simon R
Published in Microbial genomics (01.10.2017)
Published in Microbial genomics (01.10.2017)
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Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
Argimón, Silvia, Abudahab, Khalil, Goater, Richard J. E., Fedosejev, Artemij, Bhai, Jyothish, Glasner, Corinna, Feil, Edward J., Holden, Matthew T. G., Yeats, Corin A., Grundmann, Hajo, Spratt, Brian G., Aanensen, David M.
Published in Microbial genomics (01.11.2016)
Published in Microbial genomics (01.11.2016)
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chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
Silva, Mickael, Machado, Miguel P., Silva, Diogo N., Rossi, Mirko, Moran-Gilad, Jacob, Santos, Sergio, Ramirez, Mario, Carriço, João André
Published in Microbial genomics (01.03.2018)
Published in Microbial genomics (01.03.2018)
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Identification of Klebsiella capsule synthesis loci from whole genome data
Wyres, Kelly L., Wick, Ryan R., Gorrie, Claire, Jenney, Adam, Follador, Rainer, Thomson, Nicholas R., Holt, Kathryn E.
Published in Microbial genomics (01.12.2016)
Published in Microbial genomics (01.12.2016)
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Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive
Wyres, Kelly L., Cahill, Sarah M., Holt, Kathryn E., Hall, Ruth M., Kenyon, Johanna J.
Published in Microbial genomics (01.03.2020)
Published in Microbial genomics (01.03.2020)
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Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations
Lam, Margaret M. C., Wick, Ryan R., Wyres, Kelly L., Gorrie, Claire L., Judd, Louise M., Jenney, Adam W. J., Brisse, Sylvain, Holt, Kathryn E.
Published in Microbial genomics (01.09.2018)
Published in Microbial genomics (01.09.2018)
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Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores
Schwengers, Oliver, Barth, Patrick, Falgenhauer, Linda, Hain, Torsten, Chakraborty, Trinad, Goesmann, Alexander
Published in Microbial genomics (01.10.2020)
Published in Microbial genomics (01.10.2020)
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Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Pérez-Cobas, Ana Elena, Gomez-Valero, Laura, Buchrieser, Carmen
Published in Microbial genomics (01.08.2020)
Published in Microbial genomics (01.08.2020)
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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
De Maio, Nicola, Shaw, Liam P., Hubbard, Alasdair, George, Sophie, Sanderson, Nicholas D., Swann, Jeremy, Wick, Ryan, AbuOun, Manal, Stubberfield, Emma, Hoosdally, Sarah J., Crook, Derrick W., Peto, Timothy E. A., Sheppard, Anna E., Bailey, Mark J., Read, Daniel S., Anjum, Muna F., Walker, A. Sarah, Stoesser, Nicole
Published in Microbial genomics (01.09.2019)
Published in Microbial genomics (01.09.2019)
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Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history
Coscolla, Mireia, Gagneux, Sebastien, Menardo, Fabrizio, Loiseau, Chloé, Ruiz-Rodriguez, Paula, Borrell, Sonia, Otchere, Isaac Darko, Asante-Poku, Adwoa, Asare, Prince, Sánchez-Busó, Leonor, Gehre, Florian, Sanoussi, C. N’Dira, Antonio, Martin, Affolabi, Dissou, Fyfe, Janet, Beckert, Patrick, Niemann, Stefan, Alabi, Abraham S., Grobusch, Martin P., Kobbe, Robin, Parkhill, Julian, Beisel, Christian, Fenner, Lukas, Böttger, Erik C., Meehan, Conor J., Harris, Simon R., de Jong, Bouke C., Yeboah-Manu, Dorothy, Brites, Daniela
Published in Microbial genomics (01.02.2021)
Published in Microbial genomics (01.02.2021)
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Genome-scale rates of evolutionary change in bacteria
Duchêne, Sebastian, Holt, Kathryn E., Weill, François-Xavier, Le Hello, Simon, Hawkey, Jane, Edwards, David J., Fourment, Mathieu, Holmes, Edward C.
Published in Microbial genomics (01.11.2016)
Published in Microbial genomics (01.11.2016)
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