.gitignore
CITATION.cff
LICENSE.md
README.md
_config.yml
pyproject.toml
arvia/__init__.py
arvia/arvia.py
arvia.egg-info/PKG-INFO
arvia.egg-info/SOURCES.txt
arvia.egg-info/dependency_links.txt
arvia.egg-info/entry_points.txt
arvia.egg-info/requires.txt
arvia.egg-info/top_level.txt
arvia/data/arvia.drawio
arvia/data/arvia_header_bb.png
arvia/data/arvia_header_wb.png
arvia/data/arvia_icon.png
arvia/data/arvia_sp_v0.1.1.png
arvia/data/examples/example_arvia_result.png
arvia/data/examples/example_arvia_sc_result.png
arvia/data/examples/example_big_insertion.png
arvia/data/examples/example_big_insertion_with_soft_clips.png
arvia/data/examples/example_missing_feature.png
arvia/data/examples/example_mixed_position.png
arvia/data/examples/example_result.xlsx
arvia/data/examples/example_result_sc.xlsx
arvia/data/genes/paeruginosa_oprd/GCF_000006765.1_ASM676v1_genomic_oprD.gb
arvia/data/genes/paeruginosa_oprd/Pseudomonas_aeruginosa_F23197_6110_oprD.gb
arvia/data/genes/paeruginosa_oprd/Pseudomonas_aeruginosa_FRD1_2621_oprD.gb
arvia/data/genes/paeruginosa_oprd/Pseudomonas_aeruginosa_LESB58_125_oprD.gb
arvia/data/genes/paeruginosa_oprd/Pseudomonas_aeruginosa_MTB-1_210_oprD.gb
arvia/data/genes/paeruginosa_oprd/Pseudomonas_aeruginosa_UCBPP-PA14_109_oprD.gb
arvia/data/genes/paeruginosa_oprd/oprD.ffn
arvia/data/genomes/Pseudomonas_aeruginosa_PAO1_107.gbk
arvia/envs/arvia.yml
arvia/scripts/snippy-vcf_to_tab
arvia/scripts/snippy_add_missing_features.sh
arvia/utils/aeruginosa_polymorphisms.py
arvia/utils/aeruginosa_snippy.py
arvia/utils/aeruginosa_truncations.py
arvia/utils/annotation_extraction.py
arvia/utils/combine_snippy_results.py
arvia/utils/console_log.py
arvia/utils/local_paths.py
arvia/utils/prepare_files_for_igvreport.py
arvia/utils/process_amrfinder.py
arvia/utils/process_mlst.py
arvia/utils/process_snippy_one_to_one.py
arvia/utils/process_user_input.py
arvia/utils/snakemake_common.py
arvia/utils/test_pipeline.py
arvia/utils/user_parser.py
arvia/workflows/arvia.smk
arvia/workflows/dbs.smk