├── .github └── workflows │ └── runTest.yml ├── .gitignore ├── CONTRIBUTING_GUIDELINE.md ├── Dockerfile ├── LICENSE.txt ├── MANIFEST.in ├── Makefile ├── README.md ├── codecov.yml ├── conda_recipe └── meta.yaml ├── demo ├── query_data │ └── query_data.fq ├── query_data_random │ └── random.fq ├── readme.md ├── ref_genomes │ ├── GCF_018918045.1_genomic.fna.gz │ ├── GCF_018918095.1_genomic.fna.gz │ ├── GCF_018918125.1_genomic.fna.gz │ ├── GCF_018918185.1_genomic.fna.gz │ ├── GCF_018918235.1_genomic.fna.gz │ ├── GCF_018918285.1_genomic.fna.gz │ ├── GCF_018918345.1_genomic.fna.gz │ ├── GCF_907163105.1_genomic.fna.gz │ ├── GCF_907163115.1_genomic.fna.gz │ ├── GCF_907163125.1_genomic.fna.gz │ ├── GCF_907163135.1_genomic.fna.gz │ ├── GCF_907164845.1_genomic.fna.gz │ ├── GCF_907164905.1_genomic.fna.gz │ ├── GCF_907165045.1_genomic.fna.gz │ └── GCF_907165215.1_genomic.fna.gz └── toy_genome_to_taxid.tsv ├── depreciated └── old_code.py ├── docs ├── column_descriptions.csv └── wiki │ ├── readme.md │ └── yacht_alg_annotation.pdf ├── env └── yacht_env.yml ├── pyproject.toml ├── ruff.toml ├── setup.py ├── src ├── cpp │ ├── argparse.hpp │ ├── json.hpp │ └── main.cpp └── yacht │ ├── __init__.py │ ├── download_default_ref_db.py │ ├── download_demofiles.py │ ├── download_pretrained_ref_db.py │ ├── hypothesis_recovery_src.py │ ├── make_training_data_from_sketches.py │ ├── run_YACHT.py │ ├── sketch_ref_genomes.py │ ├── sketch_sample.py │ ├── standardize_yacht_output.py │ └── utils.py ├── tests ├── profiling │ └── for_profiling.py ├── test_download_default_ref_db.py ├── test_download_demofiles.py ├── test_download_pretrained_ref_db.py ├── test_hypothesis_recovery_src.py ├── test_make_training_data_from_sketches.py ├── test_sketch_ref_genomes.py ├── test_sketch_sample.py ├── test_standardize_output.py ├── test_unit.py ├── test_unittests.py ├── test_utils.py ├── test_utils_for_bug_YAC-13.py ├── test_utils_other.py ├── test_workflow.py ├── test_y_integration_tests.py ├── testdata │ ├── 20_genomes_sketches.zip │ ├── integration_test_hash_to_col_idx.pkl │ ├── sample.sig.zip │ ├── sample_cami.txt │ └── standardize_output_testdata │ │ ├── cami_result.cami │ │ ├── result.xlsx │ │ └── toy_genome_to_taxid.tsv ├── testdata_bug_YAC13 │ └── extract_empty_hash.sig.zip └── unittests_data │ ├── test_collect_signature_info_data.json │ └── test_tmp │ ├── empty_hash_to_col_idx.pkl │ ├── existing_file.txt │ └── hash_to_col_idx.pkl └── use_case_examples ├── MAG_fishing ├── README.md ├── data_download.sh ├── result_k51_ani0.95_SRR32008482.xlsx ├── venn.png └── venn.py ├── README.md ├── low_abundance_samples ├── README.md ├── data_download.sh ├── result_k21_ani0.95.xlsx ├── result_k31_ani0.90.xlsx ├── result_k31_ani0.95.xlsx ├── result_k31_ani0.9995.xlsx ├── result_k51_ani0.95.xlsx ├── venn_ani.py ├── venn_ksize.py ├── venn_low_abundance_species_ani.png └── venn_low_abundance_species_ksize.png └── synthetic_metagenome ├── README.md ├── matched_identifiers.tab ├── venn.py ├── 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