.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
LICENSE
README.md
binette.yaml
pyproject.toml
.github/workflows/binette_ci.yml
.github/workflows/build_draft_pdf.yml
.github/workflows/check_conda_recipe.yml
.github/workflows/lint_and_format.yml
.github/workflows/release.yml
.github/workflows/test_tutorial_environment.yml
Binette.egg-info/PKG-INFO
Binette.egg-info/SOURCES.txt
Binette.egg-info/dependency_links.txt
Binette.egg-info/entry_points.txt
Binette.egg-info/requires.txt
Binette.egg-info/top_level.txt
binette/__init__.py
binette/bin_manager.py
binette/bin_quality.py
binette/cds.py
binette/contig_manager.py
binette/diamond.py
binette/io_manager.py
binette/main.py
docs/Makefile
docs/conf.py
docs/contributing.md
docs/index.md
docs/installation.md
docs/make.bat
docs/tests.md
docs/usage.md
docs/api/api_ref.md
docs/api/binette.md
docs/tutorial/analyse_binette_result.ipynb
docs/tutorial/assembly.md
docs/tutorial/binette.md
docs/tutorial/binette_tutorial_env.yaml
docs/tutorial/binning.md
docs/tutorial/get_dataset.md
docs/tutorial/set_environment.md
docs/tutorial/tutorial_main.md
docs/tutorial/binette_output/final_bins_quality_reports.tsv
docs/tutorial/binette_output/input_bins_quality_reports/input_bins_1.concoct_bins.tsv
docs/tutorial/binette_output/input_bins_quality_reports/input_bins_2.maxbin2.tsv
docs/tutorial/binette_output/input_bins_quality_reports/input_bins_2.maxbin2_bins.tsv
docs/tutorial/binette_output/input_bins_quality_reports/input_bins_3.metabat2.tsv
docs/tutorial/binette_output/input_bins_quality_reports/input_bins_3.metabat2_bins.tsv
docs/tutorial/binette_output/input_bins_quality_reports/input_bins_4.semibin2_output_bins.tsv
docs/tutorial/binette_output/input_bins_quality_reports/input_bins_4.semibin2_output_output_bins.tsv
docs/tutorial/sbatch_scripts/01_download_dataset.sbatch
docs/tutorial/sbatch_scripts/02_assembly.sbatch
docs/tutorial/sbatch_scripts/03_read_alignment.sbatch
docs/tutorial/sbatch_scripts/04_binning.sbatch
docs/tutorial/sbatch_scripts/05_binette.sbatch
docs/tutorial/sbatch_scripts/06_analysis.sbatch
docs/tutorial/sbatch_scripts/README.md
docs/tutorial/sbatch_scripts/submit_tutorial_pipeline.sbatch
docs/tutorial/snippets/01_download_dataset.sh
docs/tutorial/snippets/02_assembly.sh
docs/tutorial/snippets/03_read_alignment.sh
docs/tutorial/snippets/04a_binning_metabat2.sh
docs/tutorial/snippets/04b_binning_maxbin2.sh
docs/tutorial/snippets/04c_binning_concoct.sh
docs/tutorial/snippets/04d_binning_semibin2.sh
docs/tutorial/snippets/05_binette.sh
paper/binette_overview.pdf
paper/paper.bib
paper/paper.md
tests/__init__.py
tests/conftest.py
tests/expected_results/final_bins_quality_reports.tsv
tests/expected_results/final_bins_quality_reports_from_proteins_input.tsv
tests/functional_tests/test_binette_command.py
tests/unit_tests/__init__.py
tests/unit_tests/bin_manager_test.py
tests/unit_tests/bin_quality_test.py
tests/unit_tests/cds_test.py
tests/unit_tests/contig_manager_test.py
tests/unit_tests/contigs.fasta
tests/unit_tests/diamonds_test.py
tests/unit_tests/io_manager_test.py
tests/unit_tests/main_binette_test.py