├── .github └── workflows │ └── github-actions.yaml ├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.rst ├── galaxy └── Galaxy-Workflow-Assembly-Serotyping-withReport-for-SISTR_v1.1.1+galaxy1-recipe.ga ├── setup.py ├── sistr ├── __init__.py ├── data │ └── serovar-list.txt ├── misc │ ├── __init__.py │ ├── add_ref_genomes.py │ ├── csv_to_hdf.py │ ├── hc_clusters_from_cgmlst_profiles.py │ └── reduce_to_centroid_alleles.py ├── sistr_cmd.py ├── src │ ├── __init__.py │ ├── blast_wrapper │ │ ├── __init__.py │ │ └── helpers.py │ ├── cgmlst │ │ ├── __init__.py │ │ ├── extras │ │ │ ├── __init__.py │ │ │ ├── centroid_cgmlst_alleles.py │ │ │ └── hclust_cutree.py │ │ └── msa.py │ ├── logger.py │ ├── mash.py │ ├── parsers.py │ ├── qc │ │ ├── __init__.py │ │ └── constants.py │ ├── serovar_prediction │ │ ├── __init__.py │ │ └── constants.py │ └── writers.py └── version.py └── tests ├── 00_0163.fasta ├── conftest.py ├── test_cgmlst.py ├── test_hclust_cutree.py ├── test_mash.py ├── 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