LICENSE
README.md
setup.py
cap2/__init__.py
cap2/api.py
cap2/cli.py
cap2/constants.py
cap2/exceptions.py
cap2/sample.py
cap2/setup_logging.py
cap2/utils.py
cap2.egg-info/PKG-INFO
cap2.egg-info/SOURCES.txt
cap2.egg-info/dependency_links.txt
cap2.egg-info/entry_points.txt
cap2.egg-info/requires.txt
cap2.egg-info/top_level.txt
cap2/capalyzer/__init__.py
cap2/capalyzer/cli.py
cap2/capalyzer/exceptions.py
cap2/capalyzer/parsers.py
cap2/capalyzer/version.py
cap2/capalyzer/pangea/__init__.py
cap2/capalyzer/pangea/api.py
cap2/capalyzer/pangea/cli.py
cap2/capalyzer/pangea/pangea_file_source.py
cap2/capalyzer/pangea/pangea_file_uploader.py
cap2/capalyzer/pangea/parsers.py
cap2/capalyzer/pangea/utils.py
cap2/capalyzer/table_builder/__init__.py
cap2/capalyzer/table_builder/base_module.py
cap2/capalyzer/table_builder/cap_table_builder.py
cap2/capalyzer/table_builder/parsers.py
cap2/capalyzer/table_builder/modules/__init__.py
cap2/capalyzer/table_builder/modules/basic_stats_summary.py
cap2/capalyzer/table_builder/modules/covid_variant_table.py
cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py
cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py
cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py
cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py
cap2/capalyzer/table_parser/__init__.py
cap2/capalyzer/table_parser/analysis_utils.py
cap2/capalyzer/table_parser/cap_table_parser.py
cap2/extensions/__init__.py
cap2/extensions/cli.py
cap2/extensions/experimental/__init__.py
cap2/extensions/experimental/cli.py
cap2/extensions/experimental/covid/__init__.py
cap2/extensions/experimental/covid/align_to_covid_genome.py
cap2/extensions/experimental/covid/call_covid_variants.py
cap2/extensions/experimental/covid/cli.py
cap2/extensions/experimental/covid/covid_genome_db.py
cap2/extensions/experimental/covid/fast_detect.py
cap2/extensions/experimental/covid/genome_coverage.py
cap2/extensions/experimental/covid/make_covid_consensus_seq.py
cap2/extensions/experimental/covid/make_pileup.py
cap2/extensions/experimental/preclassify/__init__.py
cap2/extensions/experimental/preclassify/cli.py
cap2/extensions/experimental/preclassify/dynamic_pipeline.py
cap2/extensions/experimental/preclassify/preclassify.py
cap2/extensions/experimental/preclassify/preclassify_db.py
cap2/extensions/experimental/strains/__init__.py
cap2/extensions/experimental/strains/align_to_genome.py
cap2/extensions/experimental/strains/align_to_genome_db.py
cap2/extensions/experimental/strains/bacterial_genome_getter.py
cap2/extensions/experimental/strains/cli.py
cap2/extensions/experimental/strains/get_microbial_genome.py
cap2/extensions/experimental/strains/make_pileup.py
cap2/extensions/experimental/strains/make_snp_clusters.py
cap2/extensions/experimental/strains/make_snp_graph.py
cap2/extensions/experimental/strains/make_snp_table.py
cap2/extensions/experimental/strains/merge_snp_clusters.py
cap2/extensions/experimental/strains/merge_snp_graph.py
cap2/extensions/experimental/strains/tasks.py
cap2/extensions/experimental/strains/utils.py
cap2/extensions/experimental/strains/strainotyping/__init__.py
cap2/extensions/experimental/strains/strainotyping/api.py
cap2/extensions/experimental/strains/strainotyping/cli.py
cap2/extensions/experimental/strains/strainotyping/clustering.py
cap2/extensions/experimental/strains/strainotyping/graphs.py
cap2/extensions/experimental/strains/strainotyping/io.py
cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py
cap2/extensions/experimental/tcems/__init__.py
cap2/extensions/experimental/tcems/cli.py
cap2/extensions/experimental/tcems/mixcr.py
cap2/extensions/experimental/tcems/tcem_aa_db.py
cap2/extensions/experimental/tcems/tcem_repertoire.py
cap2/pangea/__init__.py
cap2/pangea/api.py
cap2/pangea/cli.py
cap2/pangea/cli_utils.py
cap2/pangea/constants.py
cap2/pangea/download_reads.py
cap2/pangea/load_task.py
cap2/pangea/pangea_sample.py
cap2/pangea/sra_utils.py
cap2/pangea/utils.py
cap2/pipeline/__init__.py
cap2/pipeline/config.py
cap2/pipeline/constants.py
cap2/pipeline/full_pipeline.py
cap2/pipeline/assembly/__init__.py
cap2/pipeline/assembly/clean_contigs.py
cap2/pipeline/assembly/metabat2.py
cap2/pipeline/assembly/metaspades.py
cap2/pipeline/contigs/__init__.py
cap2/pipeline/contigs/amr_identification.py
cap2/pipeline/contigs/prodigal.py
cap2/pipeline/databases/__init__.py
cap2/pipeline/databases/amr_db.py
cap2/pipeline/databases/fast_kraken2_db.py
cap2/pipeline/databases/hmp_db.py
cap2/pipeline/databases/human_removal_db.py
cap2/pipeline/databases/kraken2_db.py
cap2/pipeline/databases/mouse_removal_db.py
cap2/pipeline/databases/taxonomic_db.py
cap2/pipeline/databases/uniref.py
cap2/pipeline/preprocessing/__init__.py
cap2/pipeline/preprocessing/base_reads.py
cap2/pipeline/preprocessing/basic_sample_stats.py
cap2/pipeline/preprocessing/clean_reads.py
cap2/pipeline/preprocessing/control_sample_abundances.py
cap2/pipeline/preprocessing/count_reads.py
cap2/pipeline/preprocessing/error_correct_reads.py
cap2/pipeline/preprocessing/fast_taxa.py
cap2/pipeline/preprocessing/fastqc.py
cap2/pipeline/preprocessing/map_to_human.py
cap2/pipeline/preprocessing/map_to_mouse.py
cap2/pipeline/preprocessing/multiqc.py
cap2/pipeline/preprocessing/remove_adapters.py
cap2/pipeline/short_read/__init__.py
cap2/pipeline/short_read/amrs.py
cap2/pipeline/short_read/hmp_comparison.py
cap2/pipeline/short_read/humann2.py
cap2/pipeline/short_read/jellyfish.py
cap2/pipeline/short_read/kraken2.py
cap2/pipeline/short_read/mash.py
cap2/pipeline/short_read/microbe_census.py
cap2/pipeline/short_read/processed_reads.py
cap2/pipeline/short_read/read_stats.py
cap2/pipeline/utils/__init__.py
cap2/pipeline/utils/cap_task.py
cap2/pipeline/utils/conda.py
cap2/pipeline/utils/utils.py
tests/__init__.py
tests/test_api.py
tests/test_assembly.py
tests/test_databases.py
tests/test_experimental_covid.py
tests/test_experimental_strain.py
tests/test_pangea.py
tests/test_pipeline_preprocessing.py
tests/test_short_read.py
tests/test_strainotyping.py
tests/test_tcems.py
tests/test_versions.py