> 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/technical-descriptions-of-analysis-tools/change-log.md).

# Change log

#### `alignment-2697049-1`

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#### `amrfinder-1280-4`

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#### `amrfinder-1313-2`

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#### `amrfinder-1352-2`

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#### `amrfinder-194-2`

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#### `amrfinder-287-3`

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#### `amrfinder-354276-2`

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#### `amrfinder-470-3`

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#### `amrfinder-485-3`

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#### `amrfinder-562-2`

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#### `amrfinder-573-2`

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#### `amrfinder-590-2`

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#### `amrfinder-620-2`

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#### `amrfinder-727-2`

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#### `assembly-1`

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#### `cgmlst-1280-2`

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#### `cgmlst-1313-1`

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#### `cgmlst-1352-1`

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#### `cgmlst-1639-1`

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#### `cgmlst-1773-1`

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#### `cgmlst-195-1`

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#### `cgmlst-197-1`

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#### `cgmlst-287-1`

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#### `cgmlst-28901-3`

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#### `cgmlst-470-1`

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#### `cgmlst-485-1`

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#### `cgmlst-562-1`

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#### `cgmlst-573-2`

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#### `cgmlst-666-1`

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#### `cgmlst-727-1`

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#### `clermontyping-562-1`

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#### `clustering-cgmlst-3`

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#### `core-1280-1`

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#### `core-1336-1`

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#### `core-1463165-1`

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#### `core-1646-1`

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#### `core-244366-1`

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#### `core-28901-1`

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#### `core-485-1`

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#### `core-498019-1`

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#### `core-573-1`

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#### `core-64320-1`

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#### `core-666-1`

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#### `core-90370-1`

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#### `ectyper-562-1`

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#### `genotyphi-90370-1`

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#### `hclink-562-3`

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#### `hclink-562-4`

Release date: 2025-12-01

Docker image: [`hclink:4.0.1-ecoli-2025_11_27`](https://github.com/pathogenwatch/docs/blob/main/technical-descriptions-of-analysis-tools/registry.gitlab.com/cgps/pathogenwatch-tasks/hclink:4.0.1-ecoli-2025_11_27@sha256:4045a87120b2ed85ddce19d825672b0fa20368cc02cb2ee19aea136f20d6473c).

Switched to using exact search mode in unum-usearch due to a small percentage of genomes not being assigned the nearest profile by heueristic mode searches.

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#### `hclink-28901-3`

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#### `hclink-28901-4`

Release date: 2025-12-01

Docker image: [`hclink:4.0.1-senterica-2025_11_27`](https://github.com/pathogenwatch/docs/blob/main/technical-descriptions-of-analysis-tools/registry.gitlab.com/cgps/pathogenwatch-tasks/hclink:4.0.1-senterica-2025_11_27@sha256:9723164ac211f129e24502ac88f2d2eacbfeebd8eaa4eacd83ea2d5eb84ea7c3).

Switched to using same method as *E. coli*.

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#### `kaptive-470-1`

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#### `kaptive-470-2` 

Release date: 2026-07-08

Updated to Kaptive v3.2.1

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#### `kaptive-3390273-2` 

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#### `kaptive-3390273-3` 

Release date: 2026-07-08

Updated to Kaptive v3.2.1

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#### `kaptive-571-1` 

Release date: 2026-07-08

Kaptive v3.2.1 + K. oxytoca libraries v1.0.0

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#### `kleborate-548-3`

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#### `kleborate-571-3`

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#### `kleborate-3390273-3`

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#### `lincodes-3390273-1` 

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#### `lincodes-3390273-2` 

Release date: 2026-07-13

Database update 2026-07-07

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#### `metrics-2`

Release date: 2025-06-12

Assembly stats are now produced by [QUAST](https://github.com/ablab/quast) v5.3.0 (provided by [staphb/quast:5.3.0](https://hub.docker.com/layers/staphb/quast/5.3.0/images/sha256-e885c646124d099fe29ad05e223a0d7c9410c90dd70b4abadf63d34d158e5eeb)).

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#### `mlst-1280-4` 

Release date: 2026-07-01

Scheme ID: 2026-05-12-saureus

Updated the MLST database.

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#### `mlst-1313-3` 

Release date: 2026-07-01

Scheme ID: 2026-05-12-spneumoniae

Updated the MLST database.

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#### `mlst-1336-3`

Release date: 2026-07-01

Scheme ID: 2026-05-12-szooepidemicus

Updated the MLST database.

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#### `mlst-1352-4`

Release date: 2026-07-01

Scheme ID: 2026-05-12-efaecium

Updated the MLST database.

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#### `mlst-1639-3`

Release date: 2026-07-01

Scheme ID: 2026-05-12-lmonocytogenes

Updated the MLST database.

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#### `mlst-195-4`

Release date: 2026-07-01

Scheme ID: 2026-05-12-campylobacter

Updated the MLST database.

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#### `mlst-197-4`

Release date: 2026-07-01

Scheme ID: 2026-05-12-campylobacter

Updated the MLST database.

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#### `mlst-287-4`

Release date: 2026-07-01

Scheme ID: 2026-05-12-paeruginosa

Updated the MLST database.

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#### `mlst-28901-6`

Release date: 2026-07-01

Scheme ID: 2026-05-12-senterica

Updated the MLST database.

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#### `mlst-3390273-3`

Release date: 2026-07-01

Scheme ID: 2026-05-12-kpneumoniae

Updated the MLST database.

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#### `mlst-354276-4`

Release date: 2026-07-01

Scheme ID: 2026-05-12-ecloacae

Updated the MLST database.

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#### `mlst-470-3`

Release date: 2026-07-01

Scheme ID: 2026-05-12-abaumannii

Updated the MLST database.

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#### `mlst-485-3`

Release date: 2026-07-01

Scheme ID: 2026-05-12-neisseria

Updated the MLST database.

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#### `mlst-562-5`

Release date: 2026-07-01

Scheme ID: 2026-05-12-ecoli

Updated the MLST database.

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#### `mlst-571-3`

Release date: 2026-07-01

Scheme ID: 2026-05-12-koxytoca

Updated the MLST database.

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#### `mlst-666-3`

Release date: 2026-07-01

Scheme ID: 2026-05-12-vcholerae

Updated the MLST database.

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#### `mlst-727-4`

Release date: 2026-07-01

Scheme ID: 2026-05-12-hinfluenzae

Updated the MLST database.

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#### `mlst-virulence-1639-2`

Release date: 2026-07-01

Scheme ID: 2026-07-01\_lmonocytogenes\_vir

Updated the MLST database.

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#### `mlst2-470-3`

Release date: 2026-07-01

Scheme ID: 2026-06-17-abaumannii\_2

Updated the MLST database.

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#### `mlst2-562-2`

Release date: 2026-07-01

Scheme ID: 2026-06-17-ecoli\_2

Updated the MLST database.

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#### `ngmast-1`

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#### `ngono-markers-1`

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#### `ngstar-1`

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#### `paarsnp-1280-1`

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#### `paarsnp-1313-1`

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#### `paarsnp-1352-1`

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#### `paarsnp-1773-1`

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#### `paarsnp-195-1`

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#### `paarsnp-197-1`

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#### `paarsnp-485-1`

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#### `paarsnp-498019-1`

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#### `paarsnp-666-1`

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#### `paarsnp-727-1`

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#### `paarsnp-90370-1`

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#### `pangolin-1`

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#### `plasmidfinder-ebacter-1`

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#### `plasmidfinder-gp-1`

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#### `poppunk-1313-2`

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#### `poppunk-666-1`

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#### `rfplus-1639-1`

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#### `rfplus-28901-1`

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#### `rfplus-562-1`

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#### `sarscov2-variants-1`

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#### `serotype-seqsero2-1`

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#### `serotype-seroba-2`

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#### `serotype-sistr-590-2`

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#### `speciator-1`

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#### `spn-pbp-amr-1313-1`

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#### `stecfinder-1`

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#### `tree-cgmlst-1639-1`

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#### `tree-cgmlst-562-1`

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#### `tree-core-1280-1`

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#### `tree-core-1336-1`

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#### `tree-core-1463165-1`

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#### `tree-core-1646-1`

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#### `tree-core-244366-1`

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#### `tree-core-28901-1`

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#### `tree-core-485-1`

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#### `tree-core-498019-1`

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#### `tree-core-573-1`

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#### `tree-core-64320-1`

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#### `tree-core-666-1`

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#### `tree-core-90370-1`

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#### `virulencefinder-562-1`

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#### `vista-1`