> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/news-and-release-notes/release-notes-2024.md). # Release Notes 2024 ## v23.0.2 *5th November* #### Updated * The link to the Kleborate documentation from the Genome Reports has been updated to point to documentation for Kleborate 3. ## v23.0.1 *28th October* #### Fixed * A rendering error was causing *K. pneumoniae* collections not to load in the viewer. This has been fixed. ## v23.0.0 *25th October* #### Updated * All MLST schemes have been updated and the new version made available. The MLST schemes were updated on the 4th September. All genomes have been updated to the latest assignments. * The Enterobase Yersinia MLST scheme is now applied to all Yersinia genomes and not just *Y. enterolitica*. * Similarly all cgMLST schemes have been updated as well, with the schemes downloaded on the 4th of September. * We have switched to the Enterobase cgMLST scheme for *C. difficile*, replacing the previous scheme from Ridom. #### New * We have added one MLST scheme: * *C. perfringens* (Enterobase) * We have also added 13 new cgMLST schemes: * *B. anthracis* (PubMLST) * *B. cereus* (PubMLST) * *B. mallei* (PubMLST) * *Brucella* (PubMLST) * *C. perfringens* (Enterobase) * *C. trachamotis* (PubMLST) * *H. influenzae* (PubMLST) * *M. abscessus* (PubMLST) * *S. uberis* (PubMLST) * *Y. enterolitica* (Pasteur) * *Y. tuberculosis* (Pasteur) * *Other Yersinia* (Enterobase) ## v22.5.4 #### 16th October #### Updated * Minor modifications to the Kleborate and Kaptive pipelines to fix a small percentage of failures. #### Fixed * Where the Kleborate or Kaptive analyses have failed CSV files will still generate correctly. ## v22.5.0 9th October #### Updated * [Kleborate](/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/kleborate.md) has been updated to v3.1.0. It is now provided in 3 different modes, according to the species - *K. pneumoniae* species complex, *K. oxytoca* species complex, and other Klebsiella. All Klebsiella genomes have been updated to the new version: . * [Kaptive](/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/kaptive.md) has been updated to v3.0.0b5. Kaptive is now run directly on *K. pneumoniae* complex species and CSV file results are now available for download separately from the Kleborate download. All *A. baumannii* and *K. pneumoniae* complex genomes have been updated: . ## v22.3.9 *30th September* This release should improve the performance and stability of the website for all users. #### Removed Sorting by "Country", "Type", and "Organism" has been disabled on the Genome view. Sorting by "Name" and "Date" is still available, which is now indicated by three horizontal lines in the column header.
## v22.3.1 - v22.3.8 *8-9th July* These releases represent a batch of updates mostly focused on improving the stability and robustness of the platform, especially when serving larger numbers of concurrent users. #### Updated * Database server, software and drivers for improved performance #### Fixed * A set of potentially slow database queries were identified and optimised * A bug that prevented the building of trees for collections containing duplicate genomes in some cases. ## v22.3.0 *10th June* #### Updated * [*S. pneumoniae* GPSC strain assignments](https://www.pneumogen.net/gps/#/) have been updated to the v8 scheme. ## v22.2.0 *17th May* #### Added * MLST assignments using the PubMLST *E. cloacae* species complex scheme have been added for *E. chengduensis*, *E. chuandaensis* and *E. pasteurii*. The last of these species is not currently recognised by Speciator and is likely to be assigned to another member of the complex. However, MLST will should still be run for them. ## v22.1.5 *17th May* #### Updated * Internal configuration update to ensure service stability. ## v22.1.3 *15th April* #### Updated * The cgMLST profile single linkage clustering tool has been refactored to reduce memory and CPU use. There should be no impact on the results. ## v22.1.0 *20th January* #### Updated * All cgMLST assignments have been updated to the latest version of the [MLST code](https://github.com/pathogenwatch-oss/mlst), with the schemes updated to 08/12/2023. This is includes several bug fixes, and we expect some significant improvements to the cgMLST profile-base clustering. Due to the complexity of the update, if you see any issues, please do get in [touch](/pathogenwatch/report-an-issue.md). ## v22.0.0 *19th January* #### New * PopPUNK cluster assignments for *Vibrio cholerae*, provided by our Vibriowatch collaboration. All *V. cholerae* genomes have been updated to include their cluster assignment. #### Removed * After further review, the previous Vista biotype assignments have been deemed unreliable. We would recommend that users do not rely on the previous results. A new version is under development by our collaborators at the Wellcome Sanger Institute. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://cgps.gitbook.io/pathogenwatch/news-and-release-notes/release-notes-2024.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.