├── .gitignore ├── CHANGELOG.md ├── Dockerfile ├── LICENSE ├── README.md ├── docs ├── Makefile └── _source │ ├── _static │ ├── css │ │ └── custom.css │ └── figures │ │ ├── aggregated_classification.svg │ │ ├── annotate.svg │ │ ├── favicon.svg │ │ ├── find_proviruses.svg │ │ ├── logo_dark.svg │ │ ├── logo_light.svg │ │ ├── marker_classification.svg │ │ ├── nmdc_edge_logo.png │ │ ├── nn_classification.svg │ │ ├── nn_classification_1.svg │ │ ├── nn_classification_2.svg │ │ ├── nn_classification_3.svg │ │ ├── nn_classification_4.svg │ │ ├── pipeline_overview.svg │ │ ├── provirus_1.svg │ │ ├── provirus_2.svg │ │ ├── provirus_3.svg │ │ ├── provirus_4.svg │ │ ├── provirus_5.svg │ │ ├── provirus_6.svg │ │ ├── score_aggregation_1.svg │ │ ├── score_aggregation_2.svg │ │ ├── score_aggregation_3.svg │ │ ├── score_calibration.svg │ │ ├── score_calibration_1.svg │ │ ├── score_calibration_2.svg │ │ ├── score_calibration_3.png │ │ ├── score_calibration_4.png │ │ ├── summary.svg │ │ ├── taxonomic_assignment_1.svg │ │ ├── taxonomic_assignment_2.svg │ │ ├── taxonomic_assignment_3.svg │ │ └── ternary.png │ ├── conf.py │ ├── faq.md │ ├── index.md │ ├── installation.md │ ├── marker_features.md │ ├── nn_classification.md │ ├── pipeline.md │ ├── post_classification_filtering.md │ ├── provirus_identification.md │ ├── quickstart.md │ ├── score_aggregation.md │ ├── score_calibration.md │ └── taxonomic_assignment.md ├── genomad ├── __init__.py ├── _paths.py ├── aragorn.py ├── cli.py ├── data │ ├── decision_forest.ubj │ ├── nn_classifier.h5 │ ├── provirus_tagger.crfsuite │ ├── rbs_categories.tsv │ ├── score_calibration_weights.npz │ └── score_calibration_weights.py ├── database.py ├── mmseqs2.py ├── modules │ ├── __init__.py │ ├── aggregated_classification.py │ ├── annotate.py │ ├── download.py │ ├── find_proviruses.py │ ├── marker_classification.py │ ├── nn_classification.py │ ├── score_calibration.py │ └── summary.py ├── neural_network │ ├── __init__.py │ ├── igloo.py │ └── 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