├── .github └── workflows │ ├── binette_ci.yml │ ├── build_draft_pdf.yml │ ├── check_conda_recipe.yml │ ├── lint_and_format.yml │ ├── release.yml │ └── test_tutorial_environment.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── binette.yaml ├── binette ├── __init__.py ├── bin_manager.py ├── bin_quality.py ├── cds.py ├── contig_manager.py ├── diamond.py ├── io_manager.py └── main.py ├── docs ├── Makefile ├── api │ ├── api_ref.md │ └── binette.md ├── conf.py ├── contributing.md ├── index.md ├── installation.md ├── make.bat ├── tests.md ├── tutorial │ ├── analyse_binette_result.ipynb │ ├── assembly.md │ ├── binette.md │ ├── binette_output │ │ ├── final_bins_quality_reports.tsv │ │ └── input_bins_quality_reports │ │ │ ├── input_bins_1.concoct_bins.tsv │ │ │ ├── input_bins_2.maxbin2.tsv │ │ │ ├── input_bins_2.maxbin2_bins.tsv │ │ │ ├── input_bins_3.metabat2.tsv │ │ │ ├── input_bins_3.metabat2_bins.tsv │ │ │ ├── input_bins_4.semibin2_output_bins.tsv │ │ │ └── input_bins_4.semibin2_output_output_bins.tsv │ ├── binette_tutorial_env.yaml │ ├── binning.md │ ├── get_dataset.md │ ├── sbatch_scripts │ │ ├── 01_download_dataset.sbatch │ │ ├── 02_assembly.sbatch │ │ ├── 03_read_alignment.sbatch │ │ ├── 04_binning.sbatch │ │ ├── 05_binette.sbatch │ │ ├── 06_analysis.sbatch │ │ ├── README.md │ │ └── submit_tutorial_pipeline.sbatch │ ├── set_environment.md │ ├── snippets │ │ ├── 01_download_dataset.sh │ │ ├── 02_assembly.sh │ │ ├── 03_read_alignment.sh │ │ ├── 04a_binning_metabat2.sh │ │ ├── 04b_binning_maxbin2.sh │ │ ├── 04c_binning_concoct.sh │ │ ├── 04d_binning_semibin2.sh │ │ └── 05_binette.sh │ └── tutorial_main.md └── usage.md ├── paper ├── binette_overview.pdf ├── paper.bib └── paper.md ├── pyproject.toml └── tests ├── __init__.py ├── conftest.py ├── expected_results ├── final_bins_quality_reports.tsv └── final_bins_quality_reports_from_proteins_input.tsv ├── functional_tests └── 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