├── .cirrus.yml ├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── cap_env.yml ├── docker_pipeline_config.py ├── docs ├── databases.md └── modules.md ├── download_databases.py ├── pipeline_config.py ├── pipeline_definition.yml ├── recipes ├── card_recipe.py ├── centrifuge_recipe.py ├── common_macrobial_recipe.py ├── gottcha_recipe.py ├── hg38_ucsc_recipe.py ├── krakenhll_recipe.py ├── megares_recipe.py ├── methyl_recipe.py ├── minikraken_recipe.py ├── staph_aureus_n315_recipe.py ├── uniref90_recipe.py └── vfdb_recipe.py ├── requirements.txt ├── scripts ├── alpha_diversity_stats.py ├── average_genome_size_normalization.py ├── beta_diversity_stats.py ├── count_classified_reads.py ├── hmp_sites_metaphlan2 │ ├── airways.SRS011132.metaphlan2.txt │ ├── airways.SRS011132.mpa.txt │ ├── airways.SRS011263.metaphlan2.txt │ ├── airways.SRS011397.metaphlan2.txt │ ├── airways.SRS012291.metaphlan2.txt │ ├── airways.SRS012663.metaphlan2.txt │ ├── gastrointestinal.SRS011061.metaphlan2.txt │ ├── gastrointestinal.SRS011134.metaphlan2.txt │ ├── gastrointestinal.SRS011239.metaphlan2.txt │ ├── gastrointestinal.SRS011271.metaphlan2.txt │ ├── gastrointestinal.SRS011302.metaphlan2.txt │ ├── gastrointestinal.SRS011405.metaphlan2.txt │ ├── gastrointestinal.SRS011452.metaphlan2.txt │ ├── gastrointestinal.SRS011529.metaphlan2.txt │ ├── gastrointestinal.SRS011586.metaphlan2.txt │ ├── gastrointestinal.SRS012273.metaphlan2.txt │ ├── oral.SRS011140.metaphlan2.txt │ ├── oral.SRS011243.metaphlan2.txt │ ├── oral.SRS013942.metaphlan2.txt │ ├── oral.SRS013948.metaphlan2.txt │ ├── oral.SRS014475.metaphlan2.txt │ ├── oral.SRS014689.metaphlan2.txt │ ├── oral.SRS015055.metaphlan2.txt │ ├── skin.SRS013258.metaphlan2.txt │ ├── skin.SRS015381.metaphlan2.txt │ ├── skin.SRS016944.metaphlan2.txt │ ├── skin.SRS017851.metaphlan2.txt │ ├── skin.SRS019015.metaphlan2.txt │ ├── urogenital_tract.SRS014465.metaphlan2.txt │ ├── urogenital_tract.SRS015071.metaphlan2.txt │ └── urogenital_tract.SRS062752.metaphlan2.txt ├── hmp_sites_metaphlan_dists.py ├── macrobe_genomes.csv ├── microbe-directory.csv ├── microbe_directory_annotate.py ├── normalize_genes_by_ags.py ├── normalize_genes_by_depth.py ├── parse_krakenhll.py ├── quantify_geneset_alignments.py ├── quantify_macrobial.py ├── quantify_resistome_table.py ├── read_stats.py ├── summarize_kraken.py └── summarize_microbe_census.py ├── snakemake_files ├── amr_profiling │ ├── align_to_amr_genes.smk │ └── resistome_amrs.smk ├── gene_sets │ ├── align_to_sa_n315.smk │ ├── humann2_functional_profiling.smk │ ├── humann2_normalize_genes.smk │ └── quantify_macrobial.smk ├── preprocessing │ ├── adapter_removal.smk │ └── filter_human_dna.smk ├── qc │ ├── adapter_removal.smk │ └── filter_human_dna.smk ├── stats │ ├── count_31mers.smk │ ├── diversity │ │ ├── alpha_diversity_stats.smk │ │ ├── beta_diversity_stats.smk │ │ ├── mash_intersample_dists.smk │ │ └── mash_sketch.smk │ ├── finch_sketch.smk │ ├── hmp_site_dists.smk 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