LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
panpiper/__init__.py
panpiper/main.py
panpiper/test.py
panpiper/workflow.py
panpiper.egg-info/PKG-INFO
panpiper.egg-info/SOURCES.txt
panpiper.egg-info/dependency_links.txt
panpiper.egg-info/entry_points.txt
panpiper.egg-info/not-zip-safe
panpiper.egg-info/requires.txt
panpiper.egg-info/top_level.txt
panpiper/tests/__init__.py
panpiper/tests/test_main.py
panpiper/tests/test_data/__init__.py
panpiper/tests/test_scripts/__init__.py
panpiper/tests/test_scripts/filter_isolates.py
panpiper/tests/test_scripts/test_concat_amrfinder.py
panpiper/workflow/assembly.smk
panpiper/workflow/pangenome.smk
panpiper/workflow/pyseer.smk
panpiper/workflow/quality.smk
panpiper/workflow/envs/amrfinder.yml
panpiper/workflow/envs/bakta.yml
panpiper/workflow/envs/bbmap.yml
panpiper/workflow/envs/bwa.yml
panpiper/workflow/envs/checkm.yml
panpiper/workflow/envs/checkm2.yml
panpiper/workflow/envs/eggnog.yml
panpiper/workflow/envs/fastani.yml
panpiper/workflow/envs/fasttree.yml
panpiper/workflow/envs/iqtree.yml
panpiper/workflow/envs/kraken.yml
panpiper/workflow/envs/mash.yml
panpiper/workflow/envs/panaroo.yml
panpiper/workflow/envs/poppunk.yml
panpiper/workflow/envs/prokka.yml
panpiper/workflow/envs/pyseer.yml
panpiper/workflow/envs/r.yml
panpiper/workflow/envs/raxml.yml
panpiper/workflow/envs/shovill.yml
panpiper/workflow/envs/unitig.yml
panpiper/workflow/envs/virsorter.yml
panpiper/workflow/scripts/AMR_heatmap.R
panpiper/workflow/scripts/checkm-log.py
panpiper/workflow/scripts/checkm_bin-stats.py
panpiper/workflow/scripts/checkm_cat.py
panpiper/workflow/scripts/concat_amrfinder.py
panpiper/workflow/scripts/count_patterns.py
panpiper/workflow/scripts/create_list.sh
panpiper/workflow/scripts/filter_genes.R
panpiper/workflow/scripts/filter_isolates.py
panpiper/workflow/scripts/filter_kmers.R
panpiper/workflow/scripts/filter_kmers_enet.R
panpiper/workflow/scripts/kraken_reformat.py
panpiper/workflow/scripts/long_to_wide.py
panpiper/workflow/scripts/mash.smk
panpiper/workflow/scripts/move_files.sh
panpiper/workflow/scripts/nc_aa_translate.py
panpiper/workflow/scripts/phylogeny_distance.py
panpiper/workflow/scripts/phylogroup_cluster.py
panpiper/workflow/scripts/quality_report.Rmd
panpiper/workflow/scripts/quality_report.html
panpiper/workflow/scripts/setup.sh
panpiper/workflow/scripts/summarise_annotations.py
panpiper/workflow/scripts/summarise_annotations_enet.py
panpiper/workflow/scripts/wrangle_output.py