Release Notes 2022
Pathogenwatch release notes for 2022
Last updated
Pathogenwatch release notes for 2022
Last updated
21st December
Last update of the 2022. The next one is already in preparation for the New Year.
has been updated to include the new 3.5.4.1, 3.5.4.2, 3.5.4.3, 4.3.1.2.1, and 4.3.1.2.1.1 lineages. All Typhi genomes have also been updated.
19th December
, and assignments have been updated to a snapshot taken on the 14th December. All Klebsiella genomes will have been updated by 13:00 GMT.
13th December
Pangolin typing for SARS-CoV-2 has been updated to pangolin-data v1.17 and all genomes updated.
6th December
18th November
The clustering service was tweaked to support Campylobacter.
11th November
8th November
Another small performance improvement to the Genome View page.
7th November
20th October
The performance of the Genome List page has been further enhanced, and should generally load much quicker.
The list of available linked collections in the Genome List is no longer available as a top level summary. Unfortunately, the aggregation was too slow on larger accounts.
14th October
The performance of the genome list page has been improved to allow further growth.
13th October
29th September
The MLST, cgMLST and NGSTAR schemes have all been updated to a snapshot built on the 11th of September, and all genomes updated.
When there is more than one match to an MLST/cgMLST locus, if one (or more) has been assigned a code only it (or they) are selected for the final profile. This results in cleaner assignments that are more consistent with PubMLST.
The MLST/cgMLST software no longer fails when FASTA headers include tabs or other unusual characters. Genomes without previous assignments have been updated.
The cgMLST-based clustering should now be faster, and less likely to fail.
2nd September
17th August
26th July
21st July
The Kleborate AMR Genotypes table CSV download in the collection view has been fixed and now correctly reports matched elements.
21st July
The Campylobacter jejuni MLST scheme has been extended to Campylobacter coli. All C. coli genomes have been updated.
14th July
The Enterobacter cloacae scheme has been extended to the other defined species of the E. cloacae complex, and the relevant genomes updated.
The SARS-CoV-2 lineage toolPangolin has been updated to pangolin-data v1.12. All SARS-CoV-2 genomes have been updated.
11th July
Pangolin lineage assignments have been updated to Pangolin v4.1.1 and Pangolin-data v1.11. All SARS-CoV-2 genomes have been updated.
17th June
56 K. quasipneumoniae genomes used as references.
41 K. variicola genomes used as references for tree building.
All K. quasipneumoniae/variicola collections.
15th June
Several internal releases have been rolled into a single external release
A minor tweak has been made to the rendering of some Kleborate fields in the Collection View Typing table.
Internal system updates.
30th May
25th May
19th May
The header of the "core allele distribution" download has been fixed. An extra comma was appended to the first column title. The first column has also been renamed for clarity.
11th May
10th May
10th May
Corrected the validation of DOI identifiers for genome and collection metadata.
5th May
5th May
Some test data was leaking into the public website due to a bug in the "feature flag" checking.
Clustering tasks should run more promptly than previously.
28th April
27th April
Pangolin has been updated to v4.0.6 and pangolin-data v1.8. All genomes have been updated.
22nd April
Reduced maximum concurrent read assembly tasks to prevent them blocking access to compute for other tasks. This will reduce the throughput of assembly tasks overall, unfortunately they were having a disproportionate effect on resource sharing.
21st April
Internal configuration issue preventing scaling of services.
4th April
28th March
While the update is completed there will be some disruption to the service. This should end by 12pm.
21st March
14th March
GFF downloads via the data tables in the collection views are working again.
28th February
21st February
A bug was found that could lead to false positives appearing of the visualisation of AMR determinants from Kleborate in Klebsiella collections. The individual genome reports, AMR profiles in the collection view, and CSV downloads were unaffected. We've also not identified any examples of it happening with the current version of Kleborate.
10th February
4th February
3rd February
28th January
The public Klebsiella (and Roualtella) metadata was updated to use the same primary accession as the ENA, and with a more consistent set of sample metadata.
28th January
7th January
We have released a new version of that fixes an issue with the previous version sometimes erroneously mislabelling a small percentage of E. coli as Shigella sonnei. The new version has been validated against more than 150,000 E. coli, and tens of thousands of Shigella (including S. flexneri) via clustering of MLST profiles. All other assignments should remain the same, please contact us if you have any mislabelled genomes. Thanks to Julio Diaz Caballero for identifying and characterising the issue, along with subsequent validation.
The Klebsiella pneumoniae complex scheme is now also run against K. quasipneumoniae, allowing of genomes.
are now also assigned for K. quasinpeumoniae and K. africana.
assignments for SARS-CoV-2 have also been updated to pangolin-data v1.16
LIN codes, using the , are now assigned for Klebsiella pneumoniae complex species. These are, in essence, a hierarchical lineage code based on cgMLST allele distance. For genomes in a novel lineage, the nearest neighbour is identified and the code inferred to the appropriate level of similarity. For complete details, see the .
LIN codes have been applied to all currently K. pneumoniae genomes, and are available in the , and CSV downloads.
Pangolin has been updated to and . All SARS-CoV-2 genomes have been updated.
The SARS-CoV-2 lineage assignment tool has been updated to the latest version of the . As usual, all genomes have been updated to the latest version.
The SARS-CoV-2 lineage assignment tool has been updated to the latest version of the . As usual, all genomes have been updated to the latest version.
Burkholderia pseudomallei cgMLST scheme, provided by . As usual, all genomes have been updated and public genomes clustered.
Pseudomonas aeruginosa cgMLST scheme, provided by .
Acinetobacter baumannii cgMLST scheme has been migrated to the community-supported scheme.
Collection trees for Klebsiella quasipneumoniae and K. variicola. The core has been developed in collaboration with .
were added to the Collection View for Klebsiella species.
Serotype assignments from have been added to the Collection View Typing table for Salmonella species. These were previously available in the Genome Reports and main downloads.
The CSV download now reports the matched library as "Reference library".
was updated to use the new . All SARS-CoV-2 genomes have been updated to the latest assignments.
K and OC polysaccharide loci types for are now assigned using the tool and shown in the and views. CSV downloads are also available via the view.
A bug that could cause the collection view to crash if not all results had been calculated for the selected Klebsiella/Raoultella genomes.
Google analytics has been replaced with the GDPR-compliant and privacy focused . The CGPS uses a self-hosted instance, so no user data is shared with 3rd parties in any form.
2,375 Neisseria gonorrhoeae made public from the .
A bug introduced with release was causing some collections to fail to render when the metadata table was viewed (as reported ). This has been fixed.
It is now possible to provide links to literature references as either Pubmed IDs or DOI system identifiers for both and collections.
The erroneously had a check mark in the "AMR Prediction" column for SARS-CoV-2. It has been removed.
, and NG-STAR schemes were updated for relevant species. The new implementation also runs cgMLST searches significantly more quickly and produces a more consistent profile.
has been updated to .
results have been updated to v2.2.0.
The representation of the K/O locus representation from in Klebsiella genome reports has been reworded for clarity.
The E. coli MLST schemes have been extended to Shigella and with the new assignments.
A bug was found in the which caused contigs containing unusual characters in the first line of the record to be ignored. This mostly seems to affected SARS-CoV-2 genomes. A fixed version (v3) has been created and deployed. All genome records are being updated and should be fixed within a day of this release.
has been updated to pangolin 3.1.17 and pangoLEARN 2021-04-28
The has been fully integrated into Pathogenwatch and is officially out of "Beta".
has been updated to pangolin 3.1.17 and pangoLEARN 2021-12-06.
(Salmonella serotype assignment) has been updated to v1.1.1.