MANIFEST.in
README.md
setup.py
BacterialTyper/__init__.py
BacterialTyper.egg-info/PKG-INFO
BacterialTyper.egg-info/SOURCES.txt
BacterialTyper.egg-info/dependency_links.txt
BacterialTyper.egg-info/requires.txt
BacterialTyper.egg-info/top_level.txt
BacterialTyper/config/__init__.py
BacterialTyper/config/extern_progs.py
BacterialTyper/config/install_dependencies.py
BacterialTyper/config/set_config.py
BacterialTyper/config/R/R_dependencies.csv
BacterialTyper/config/R/R_package.info.txt
BacterialTyper/config/R/check_install_path.R
BacterialTyper/config/R/check_install_system.R
BacterialTyper/config/R/install_github.R
BacterialTyper/config/R/install_package.R
BacterialTyper/config/perl/IslandPath_dependencies.csv
BacterialTyper/config/perl/install_perl_packages.py
BacterialTyper/config/perl/perl_dependencies.csv
BacterialTyper/config/python/additional_python_requirements.txt
BacterialTyper/config/python/min_python_requirements.txt
BacterialTyper/config/python/module_dependencies.csv
BacterialTyper/config/python/python_requirements.txt
BacterialTyper/config/python/python_requirements_summary.csv
BacterialTyper/config/software/dependencies.csv
BacterialTyper/config/software/software_details.csv
BacterialTyper/data/BUSCO_dataset.csv
BacterialTyper/data/PubMLST_datasets.csv
BacterialTyper/data/__init__.py
BacterialTyper/data/available_Trimmomatic_adapters.fasta
BacterialTyper/data/available_Trimmomatic_adapters_info.csv
BacterialTyper/data/available_plasmids_data.txt
BacterialTyper/data/data_files.py
BacterialTyper/data/toDownload.csv
BacterialTyper/modules/MGE.py
BacterialTyper/modules/__init__.py
BacterialTyper/modules/annot.py
BacterialTyper/modules/assemble.py
BacterialTyper/modules/citation.py
BacterialTyper/modules/cluster.py
BacterialTyper/modules/config.py
BacterialTyper/modules/database.py
BacterialTyper/modules/help_info.py
BacterialTyper/modules/ident.py
BacterialTyper/modules/metadata.py
BacterialTyper/modules/phylo.py
BacterialTyper/modules/prep.py
BacterialTyper/modules/profile.py
BacterialTyper/modules/qc.py
BacterialTyper/modules/report_generation.py
BacterialTyper/modules/run.py
BacterialTyper/modules/test.py
BacterialTyper/modules/trimm.py
BacterialTyper/modules/version.py
BacterialTyper/other_tools/__init__.py
BacterialTyper/other_tools/tools.py
BacterialTyper/report/__init__.py
BacterialTyper/report/retrieve_genes.py
BacterialTyper/report/Staphylococcus/__init__.py
BacterialTyper/report/Staphylococcus/get_alleles.py
BacterialTyper/report/Staphylococcus/get_spa_typing.py
BacterialTyper/scripts/BUSCO_caller.py
BacterialTyper/scripts/MLSTar.py
BacterialTyper/scripts/__init__.py
BacterialTyper/scripts/annotation.py
BacterialTyper/scripts/ariba_caller.py
BacterialTyper/scripts/bacteriophage.py
BacterialTyper/scripts/blast_parser.py
BacterialTyper/scripts/card_trick_caller.py
BacterialTyper/scripts/database_generator.py
BacterialTyper/scripts/database_user.py
BacterialTyper/scripts/edirect_caller.py
BacterialTyper/scripts/fastqc_caller.py
BacterialTyper/scripts/functions.py
BacterialTyper/scripts/genomic_island.py
BacterialTyper/scripts/get_descendant.py
BacterialTyper/scripts/min_hash_caller.py
BacterialTyper/scripts/multiQC_report.py
BacterialTyper/scripts/phylo_parser.py
BacterialTyper/scripts/plasmidID_call.py
BacterialTyper/scripts/sampleParser.py
BacterialTyper/scripts/spades_assembler.py
BacterialTyper/scripts/species_identification_KMA.py
BacterialTyper/scripts/trimmomatic_call.py
BacterialTyper/scripts/variant_calling.py
BacterialTyper/scripts/virulence_resistance.py
main/BacterialTyper