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Update Documentation for Release #219

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Dec 13, 2024
Merged

Update Documentation for Release #219

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439a66e
Updating README
emarinier Dec 10, 2024
d53dcf8
Updating changelog.
emarinier Dec 10, 2024
d5c2d83
Update README.md
emarinier Dec 10, 2024
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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# Unreleased

* Updated the Resfinder database to use the 2024-08-06 release.
* Updated the Pointfinder database to use the 2024-08-08 release.
* The Resfinder and Pointfinder databases now use FASTA record IDs with accession numbers (ex: `pmrA` -> `pmrA_1_CP055130.1`). StarAMR has been updated to support this, but database backwards compatibility is unlikely.
* The `genes_to_exclude` is affected by the above change and must now use gene IDs that exactly match the new FASTA record IDs with accession IDs.
* Removed ARG drug key entries with "None" or missing resistance.
* The ARG drug key for salmonella acrB 717 has changed to acrB 171.

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10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -145,7 +145,7 @@ If you wish to update to the latest ResFinder, PointFinder, and PlasmidFinder da
staramr db update --update-default
```

If you wish to switch to specific git commits of either ResFinder, PointFinder, or PlasmidFinder databases you may also pass `--resfinder-commit [COMMIT]`, `--pointfinder-commit [COMMIT]`, and `--plasmidfinder-commit [COMMIT]`.
If you wish to switch to specific git commits of either ResFinder, PointFinder, or PlasmidFinder databases you may also pass `--resfinder-commit [COMMIT]`, `--pointfinder-commit [COMMIT]`, and `--plasmidfinder-commit [COMMIT]`. However, please note that because of compatibility issues arising from changes in the source databases, this functionality is largely unsupported and is unlikely to work for versions of the databases that StarAMR wasn't released with.

## Restore Database

Expand Down Expand Up @@ -245,11 +245,11 @@ By default, the ResFinder/PointFinder/PlasmidFinder genes listed in [genes_to_ex

```
gene_id
aac(6')-Iaa_1_NC_003197
ColpVC_1__JX133088
gyrA_1_CP073768.1
pmrB_1_CP051284.1
```

Please make sure to include `gene_id` in the first line. The default exclusion list can also be disabled with `--no-exclude-genes`.
Please make sure to include `gene_id` in the first line. The default exclusion list can also be disabled with `--no-exclude-genes`. Gene IDs must exactly match the FASTA record IDs provided in the source databases.

## Complex Mutations

Expand Down Expand Up @@ -504,7 +504,7 @@ Restores the default database for `staramr`.

# Caveats

This software is still a work-in-progress. In particular, not all organisms stored in the PointFinder database are supported (only *salmonella*, *campylobacter* are currently supported). Additionally, the predicted phenotypes are for microbiological resistance and *not* clinical resistance. Phenotype/drug resistance predictions are an experimental feature which is continually being improved.
This software is still a work-in-progress. In particular, not all organisms stored in the PointFinder database are supported (only *enterococcus_faecalis*, *helicobacter_pylori*, *enterococcus_faecium*, *campylobacter*, *escherichia_coli*, *salmonella* are currently supported). Additionally, the predicted phenotypes are for microbiological resistance and *not* clinical resistance. Phenotype/drug resistance predictions are an experimental feature which is continually being improved.

`staramr` only works on assembled genomes and not directly on reads. A quick genome assembler you could use is [Shovill][shovill]. Or, you may also wish to try out the [ResFinder webservice][resfinder-web], or the command-line tools [rgi][] or [ariba][] which will work on sequence reads as well as genome assemblies. You may also wish to check out the [CARD webservice][card-web].

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