├── .gitignore ├── .pylintrc ├── CHANGELOG.md ├── EukMetaSanity ├── __init__.py ├── data │ ├── __init__.py │ ├── config_generation_utils.py │ ├── data.py │ ├── data_types.py │ ├── download_parsing_functions.py │ ├── download_utils.py │ ├── mmseqs_index_types.py │ └── mmseqs_operations.py ├── download-data ├── mmseqs_taxonomy_report_parser.py └── src │ ├── __init__.py │ ├── dependencies │ ├── __init__.py │ ├── augustus │ │ ├── __init__.py │ │ ├── augustus.py │ │ ├── contig_splitter.py │ │ └── taxon_ids.py │ ├── braker │ │ ├── __init__.py │ │ └── braker.py │ ├── busco │ │ ├── __init__.py │ │ └── busco.py │ ├── emapper │ │ ├── __init__.py │ │ └── emapper.py │ ├── genemark │ │ ├── __init__.py │ │ ├── genemark.py │ │ └── prothint.py │ ├── gmap │ │ ├── __init__.py │ │ ├── gmap.py │ │ └── gmap_build.py │ ├── hisat2 │ │ ├── __init__.py │ │ ├── hisat2.py │ │ └── hisat2_build.py │ ├── kofamscan │ │ ├── __init__.py │ │ └── kofamscan.py │ ├── metaeuk │ │ ├── __init__.py │ │ └── metaeuk.py │ ├── mmseqs │ │ ├── __init__.py │ │ ├── convertalis.py │ │ ├── createdb.py │ │ ├── filtertaxseqdb.py │ │ ├── search.py │ │ └── taxonomy.py │ ├── repeat_masker │ │ ├── __init__.py │ │ ├── process_repeats.py │ │ ├── repeat_masker.py │ │ └── rmout.py │ ├── repeat_modeler │ │ ├── __init__.py │ │ ├── build_database.py │ │ └── repeat_modeler.py │ └── sambamba │ │ ├── __init__.py │ │ ├── sort.py │ │ ├── utils.py │ │ └── view.py │ ├── installer-environment.yml │ ├── refine │ ├── __init__.py │ ├── collect_input.py │ ├── environment.yml │ ├── gather_protein_evidence.py │ ├── merge_sams.py │ ├── process.py │ ├── refine-config.yaml │ ├── rnaseq-mapping.list │ ├── rnaseq.py │ ├── run_braker.py │ └── transcriptomes.py │ ├── report │ ├── __init__.py │ ├── create_mmseqs_db.py │ ├── eggnog.py │ ├── environment.yml │ ├── kofamscan.py │ ├── protein_annotation.py │ ├── quality.py │ ├── report-config.yaml │ └── rrnasearch.py │ └── run │ ├── __init__.py │ ├── abinitio_augustus.py │ ├── abinitio_genemark.py │ ├── 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