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. 2021 Apr 19;13:61. doi: 10.1186/s13073-021-00858-2

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Main workflow in Pathogenwatch. New genomes can be uploaded and combined with public data for contextualisation. The collection view allows data exploration through a combined phylogenetic tree, a map, a timeline and the metadata table, which can be switched to show typing information (multi-locus sequence typing, MLST; N. gonorrhoeae sequence typing for antimicrobial resistance, NG-STAR; and N. gonorrhoeae multi-antigen sequence typing, NG-MAST) as well as known genetic AMR mechanisms for eight antibiotics. Genome reports summarise the metadata, typing and AMR marker results for individual isolates and allow finding other close genomes in Pathogenwatch based on core genome MLST (cgMLST). SNPs: single-nucleotide polymorphisms