Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins von Croucher, Nicholas J, Page, Andrew J, Connor, Thomas R, Delaney, Aidan J, Keane, Jacqueline A, Bentley, Stephen D, Parkhill, Julian, Harris, Simon R

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Roary: rapid large-scale prokaryote pan genome analysis von Page, Andrew J, Cummins, Carla A, Hunt, Martin, Wong, Vanessa K, Reuter, Sandra, Holden, Matthew T G, Fookes, Maria, Falush, Daniel, Keane, Jacqueline A, Parkhill, Julian

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Circlator: automated circularization of genome assemblies using long sequencing reads von Hunt, Martin, Silva, Nishadi De, Otto, Thomas D, Parkhill, Julian, Keane, Jacqueline A, Harris, Simon R

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Epithelial IL-22RA1-Mediated Fucosylation Promotes Intestinal Colonization Resistance to an Opportunistic Pathogen von Pham, Tu Anh N., Clare, Simon, Goulding, David, Arasteh, Julia M., Stares, Mark D., Browne, Hilary P., Keane, Jacqueline A., Page, Andrew J., Kumasaka, Natsuhiko, Kane, Leanne, Mottram, Lynda, Harcourt, Katherine, Hale, Christine, Arends, Mark J., Gaffney, Daniel J., Dougan, Gordon, Lawley, Trevor D.

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ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads von Hunt, Martin, Mather, Alison E, Sánchez-Busó, Leonor, Page, Andrew J, Parkhill, Julian, Keane, Jacqueline A, Harris, Simon R

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SNP-sites : rapid efficient extraction of SNPs from multi-FASTA alignments von Page, Andrew J, Taylor, Ben, Delaney, Aidan J, Soares, Jorge, Seemann, Torsten, Keane, Jacqueline A, Harris, Simon R

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IVA: accurate de novo assembly of RNA virus genomes von Hunt, Martin, Gall, Astrid, Ong, Swee Hoe, Brener, Jacqui, Ferns, Bridget, Goulder, Philip, Nastouli, Eleni, Keane, Jacqueline A, Kellam, Paul, Otto, Thomas D

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A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch von Argimón, Silvia, Yeats, Corin A., Goater, Richard J., Abudahab, Khalil, Taylor, Benjamin, Underwood, Anthony, Sánchez-Busó, Leonor, Wong, Vanessa K., Dyson, Zoe A., Nair, Satheesh, Park, Se Eun, Marks, Florian, Page, Andrew J., Keane, Jacqueline A., Baker, Stephen, Holt, Kathryn E., Dougan, Gordon, Aanensen, David M.

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A retrospective investigation of the population structure and geospatial distribution of Salmonella Paratyphi A in Kathmandu, Nepal von Mylona, Elli, Pham Thanh, Duy, Keane, Jacqueline A, Dongol, Sabina, Basnyat, Buddha, Dolecek, Christiane, Voong Vinh, Phat, Tran Vu Thieu, Nga, Nguyen Thi Nguyen, To, Karkey, Abhilasha, Baker, Stephen

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Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan von Ejaz, Hasan, Wang, Nancy, Wilksch, Jonathan J, Page, Andrew J, Cao, Hanwei, Gujaran, Shruti, Keane, Jacqueline A, Lithgow, Trevor, Ul-Haq, Ikram, Dougan, Gordon, Strugnell, Richard A, Heinz, Eva

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Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus von Page, Andrew J, Keane, Jacqueline A

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The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi von Carey, Megan E., Thi Nguyen, To Nguyen, Tran, Do Hoang Nhu, Dyson, Zoe A., Keane, Jacqueline A., Pham Thanh, Duy, Mylona, Elli, Nair, Satheesh, Chattaway, Marie, Baker, Stephen

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Phenotypic variation in the lipopolysaccharide O-antigen of Salmonella Paratyphi A and implications for vaccine development von Mylona, Elli, Pereira-Dias, Joana, Keane, Jacqueline A., Karkey, Abhilasha, Dongol, Sabina, Khokhar, Fahad, Tran, Tuan-Anh, Cormie, Claire, Higginson, Ellen, Baker, Stephen

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The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries von Barquist, Lars, Mayho, Matthew, Cummins, Carla, Cain, Amy K, Boinett, Christine J, Page, Andrew J, Langridge, Gemma C, Quail, Michael A, Keane, Jacqueline A, Parkhill, Julian

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The genomes of four tapeworm species reveal adaptations to parasitism von Tsai, Isheng J., Zarowiecki, Magdalena, Holroyd, Nancy, Garciarrubio, Alejandro, Sanchez-Flores, Alejandro, Brooks, Karen L., Tracey, Alan, Bobes, Raúl J., Fragoso, Gladis, Sciutto, Edda, Aslett, Martin, Beasley, Helen, Bennett, Hayley M., Cai, Jianping, Camicia, Federico, Clark, Richard, Cucher, Marcela, De Silva, Nishadi, Day, Tim A., Deplazes, Peter, Estrada, Karel, Fernández, Cecilia, Holland, Peter W. H., Hou, Junling, Hu, Songnian, Huckvale, Thomas, Hung, Stacy S., Kamenetzky, Laura, Keane, Jacqueline A., Kiss, Ferenc, Koziol, Uriel, Lambert, Olivia, Liu, Kan, Luo, Xuenong, Luo, Yingfeng, Macchiaroli, Natalia, Nichol, Sarah, Paps, Jordi, Parkinson, John, Pouchkina-Stantcheva, Natasha, Riddiford, Nick, Rosenzvit, Mara, Salinas, Gustavo, Wasmuth, James D., Zamanian, Mostafa, Zheng, Yadong, Cai, Xuepeng, Soberón, Xavier, Olson, Peter D., Laclette, Juan P., Brehm, Klaus, Berriman, Matthew

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Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data von Page, Andrew J, De Silva, Nishadi, Hunt, Martin, Quail, Michael A, Parkhill, Julian, Harris, Simon R, Otto, Thomas D, Keane, Jacqueline A

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SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data von Epping, Lennard, van Tonder, Andries J, Gladstone, Rebecca A, The Global Pneumococcal Sequencing Consortium, Bentley, Stephen D, Page, Andrew J, Keane, Jacqueline A

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PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data von Page, Andrew J, Wailan, Alexander, Shao, Yan, Judge, Kim, Dougan, Gordon, Klemm, Elizabeth J, Thomson, Nicholas R, Keane, Jacqueline A

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Comparison of classical multi-locus sequence typing software for next-generation sequencing data von Page, Andrew J, Alikhan, Nabil-Fareed, Carleton, Heather A, Seemann, Torsten, Keane, Jacqueline A, Katz, Lee S

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Corrigendum: SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data von Epping, Lennard, van Tonder, Andries J, Gladstone, Rebecca A, The Global Pneumococcal Sequencing Consortium AanensenDavidBrandileoneMaria-Cristina C AntonioMartinAlmeidaSamanta C G CamposFranciscoCarterP E ClarkeStuart C CornickJenniferCroucherNicholasDaganRonDoiphodeSanjay H DonkorEric S EkaterinaEgorovaEserOzgen KoseogluDeanEverettFordRebeccaGladstoneRebecca A Von GottbergAnneHasanuzzamanMdHawkinsPaulinaHoPLHryniewiczWaleriaPollardAndrew J KastrinTamaraKlugmanKeith P Kwambana-AdamsBrendaLawPierraLehmannDeborahLietmanThomas M El MdaghriNaimaMoianeBenildMucaveleHelioObaroStephen K OchoaTheresa J ParagiMetkaHaouaTalldu PlessisMignonKandasamyRamaPoratNuritRavikumarK L RegueiraMabelSadowyEwaSahaSamir K ShakoorSadiaSigauqueBetuelSkoczyoskaAnnaSoo KoKwanTientcheuPeggy-EstelleTitovLeonid P TurnerPaulVeeraraghavanBalajiWolterNicoleBentleyStephen D McGeeLesleyBreimanRobert F, Bentley, Stephen D, Page, Andrew J, Keane, Jacqueline A

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