MANIFEST.in
README.md
setup.py
pacu/__init__.py
pacu/galaxy.py
pacu/map_to_ref.py
pacu/run_pacu.py
pacu/version.py
pacu/app/__init__.py
pacu/app/command.py
pacu/app/report/__init__.py
pacu/app/report/htmlbase.py
pacu/app/report/htmlcitation.py
pacu/app/report/htmlelement.py
pacu/app/report/htmlreport.py
pacu/app/report/htmlreportsection.py
pacu/app/report/htmltablecell.py
pacu/app/utils/__init__.py
pacu/app/utils/bamutils.py
pacu/app/utils/iqtreeutils.py
pacu/app/utils/loggingutils.py
pacu/app/utils/megautils.py
pacu/app/utils/reportutils.py
pacu/app/utils/snakemakeutils.py
pacu/app/utils/snpmatrixutils.py
pacu/app/utils/trimmingutils.py
pacu/app/utils/workflowutils.py
pacu/resources/figtree_template.txt
pacu/resources/snp_workflow.smk
pacu/resources/style.css
pacu/resources/citations/Bogaerts_2023-ont_outbreak.json
pacu/resources/citations/Croucher_2015-gubbins.json
pacu/resources/citations/Danecek_2021-bcftools.json
pacu/resources/citations/Kalyaanamoorthy_2017-iq_tree_model.json
pacu/resources/citations/Kumar_2018-megax.json
pacu/resources/citations/Li_2018-minimap2.json
pacu/resources/citations/Nguyen_2015-iq_tree.json
pacu/resources/citations/Quinlan_2010-bedtools.json
pacu/resources/mega/infer_ml_nucleotide_template.mao
pacu/resources/mega/model_sel_ml_nucleotide_template.mao
pacu/resources/testdata/NC_002695.2-subset.fasta
pacu/resources/testdata/phylogeny.nwk
pacu/resources/testdata/snp_matrix.fasta
pacu/resources/testdata/bam/ilmn/TIAC1151.bam
pacu/resources/testdata/bam/ilmn/TIAC1151.bam.bai
pacu/resources/testdata/bam/ilmn/TIAC1153.bam
pacu/resources/testdata/bam/ilmn/TIAC1153.bam.bai
pacu/resources/testdata/bam/ilmn/TIAC1660.bam
pacu/resources/testdata/bam/ilmn/TIAC1660.bam.bai
pacu/resources/testdata/bam/ont/TIAC1151-R10-ds.bam
pacu/resources/testdata/bam/ont/TIAC1151-R10-ds.bam.bai
pacu/resources/testdata/bam/ont/TIAC1638-R9-ds.bam
pacu/resources/testdata/bam/ont/TIAC1638-R9-ds.bam.bai
pacu/resources/testdata/fastq/TIAC1151-ont.fastq.gz
pacu/resources/testdata/fastq/TIAC1151_1P.fastq.gz
pacu/resources/testdata/fastq/TIAC1151_2P.fastq.gz
pacu/resources/testdata/mega/model_selection_output.csv
pacu/resources/testdata/vcfs/TIAC1151.vcf
pacu/resources/testdata/vcfs/TIAC1152.vcf
pacu/resources/testdata/vcfs/TIAC1153.vcf
pacu/resources/testdata/vcfs/TIAC1638.vcf
pacu/tests/__init__.py
pacu/tests/test_bamutils.py
pacu/tests/test_iqtreeutils.py
pacu/tests/test_map_to_ref.py
pacu/tests/test_megautils.py
pacu/tests/test_snpmatrixutils.py
pacu/tests/test_workflow.py
pacu/tests/test_workflowutils.py
pacu_snp.egg-info/PKG-INFO
pacu_snp.egg-info/SOURCES.txt
pacu_snp.egg-info/dependency_links.txt
pacu_snp.egg-info/entry_points.txt
pacu_snp.egg-info/requires.txt
pacu_snp.egg-info/top_level.txt