.gitignore
LICENSE
MANIFEST.in
README.md
package.sh
setup.py
maginator/__init__.py
maginator/controller.py
maginator/main.py
maginator/messages.py
maginator/workflow.py
maginator.egg-info/PKG-INFO
maginator.egg-info/SOURCES.txt
maginator.egg-info/dependency_links.txt
maginator.egg-info/entry_points.txt
maginator.egg-info/not-zip-safe
maginator.egg-info/requires.txt
maginator.egg-info/top_level.txt
maginator/recommended_workflow/reads_to_bins.Snakefile
maginator/recommended_workflow/envs/checkm.yaml
maginator/recommended_workflow/envs/import_hg_19.R
maginator/recommended_workflow/envs/metabat2.yaml
maginator/recommended_workflow/envs/preprocess.yaml
maginator/recommended_workflow/envs/samtools.yaml
maginator/recommended_workflow/envs/vamb.yaml
maginator/test_data/clusters.tsv
maginator/test_data/contigs.fasta.gz
maginator/test_data/reads.csv
maginator/workflow/01_filter.Snakefile
maginator/workflow/02_gtdbtk.Snakefile
maginator/workflow/03_parse_gtdbtk.Snakefile
maginator/workflow/04_filter_geneclusters.Snakefile
maginator/workflow/05_gene_count_mat.Snakefile
maginator/workflow/06_prescreening_genes.Snakefile
maginator/workflow/07_signature_genes.Snakefile
maginator/workflow/08_outgroup.Snakefile
maginator/workflow/09_pileup.Snakefile
maginator/workflow/10_pileup_parse.Snakefile
maginator/workflow/11_alignment.Snakefile
maginator/workflow/12_phylo.Snakefile
maginator/workflow/13_gene_tax.Snakefile
maginator/workflow/benchmark.Snakefile
maginator/workflow/functional.Snakefile
maginator/workflow/reads_to_bins.Snakefile
maginator/workflow/signature_reads.Snakefile
maginator/workflow/envs/filter_geneclusters.yaml
maginator/workflow/envs/filter_geneclusters.yaml.BACKUP.6404.yaml
maginator/workflow/envs/filter_geneclusters.yaml.BASE.6404.yaml
maginator/workflow/envs/filter_geneclusters.yaml.LOCAL.6404.yaml
maginator/workflow/envs/filter_geneclusters.yaml.REMOTE.6404.yaml
maginator/workflow/envs/filter_gtdbtk.yaml
maginator/workflow/envs/phylo.yaml
maginator/workflow/envs/signature_genes.yaml
maginator/workflow/envs/signature_reads.yaml
maginator/workflow/scripts/Functions_v4.R
maginator/workflow/scripts/MGS_counts.R
maginator/workflow/scripts/SG_refinement.R
maginator/workflow/scripts/abundance_profiles.R
maginator/workflow/scripts/allele_frequency_mat.R
maginator/workflow/scripts/benchmark.py
maginator/workflow/scripts/concat.py
maginator/workflow/scripts/extract_coverage.py
maginator/workflow/scripts/filter.py
maginator/workflow/scripts/functional_profiling.R
maginator/workflow/scripts/gene_cluster2tax.py
maginator/workflow/scripts/gene_refinement_plots.R
maginator/workflow/scripts/marker_genes.py
maginator/workflow/scripts/matrix2SG_formatconversion.R
maginator/workflow/scripts/modify_gene_count_matrix.R
maginator/workflow/scripts/mpileup.py
maginator/workflow/scripts/parse_gtdbtk.py
maginator/workflow/scripts/prescreening_genes.R
maginator/workflow/scripts/sort_gene_mat.py
maginator/workflow/scripts/species_collections.py
maginator/workflow/scripts/synteny.py