├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── maginator ├── __init__.py ├── controller.py ├── main.py ├── messages.py ├── recommended_workflow │ ├── envs │ │ ├── checkm.yaml │ │ ├── import_hg_19.R │ │ ├── metabat2.yaml │ │ ├── preprocess.yaml │ │ ├── samtools.yaml │ │ └── vamb.yaml │ └── reads_to_bins.Snakefile ├── test_data │ ├── clusters.tsv │ ├── contigs.fasta.gz │ └── reads.csv ├── workflow.py └── workflow │ ├── 01_filter.Snakefile │ ├── 02_gtdbtk.Snakefile │ ├── 03_parse_gtdbtk.Snakefile │ ├── 04_filter_geneclusters.Snakefile │ ├── 05_gene_count_mat.Snakefile │ ├── 06_prescreening_genes.Snakefile │ ├── 07_signature_genes.Snakefile │ ├── 08_outgroup.Snakefile │ ├── 09_pileup.Snakefile │ ├── 10_pileup_parse.Snakefile │ ├── 11_alignment.Snakefile │ ├── 12_phylo.Snakefile │ ├── 13_gene_tax.Snakefile │ ├── benchmark.Snakefile │ ├── envs │ ├── filter_geneclusters.yaml │ ├── filter_geneclusters.yaml.BACKUP.6404.yaml │ ├── filter_geneclusters.yaml.BASE.6404.yaml │ ├── filter_geneclusters.yaml.LOCAL.6404.yaml │ ├── filter_geneclusters.yaml.REMOTE.6404.yaml │ ├── filter_gtdbtk.yaml │ ├── phylo.yaml │ ├── signature_genes.yaml │ └── signature_reads.yaml │ ├── functional.Snakefile │ ├── reads_to_bins.Snakefile │ ├── scripts │ ├── Functions_v4.R │ ├── MGS_counts.R │ ├── SG_refinement.R │ ├── abundance_profiles.R │ ├── allele_frequency_mat.R │ ├── benchmark.py │ ├── concat.py │ ├── extract_coverage.py │ ├── filter.py │ ├── functional_profiling.R │ ├── gene_cluster2tax.py │ ├── gene_refinement_plots.R │ ├── marker_genes.py │ ├── matrix2SG_formatconversion.R │ ├── modify_gene_count_matrix.R │ ├── mpileup.py │ ├── parse_gtdbtk.py │ ├── prescreening_genes.R │ ├── sort_gene_mat.py │ ├── species_collections.py │ └── synteny.py │ └── signature_reads.Snakefile ├── package.sh └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Russel88/MAGinator/HEAD/.gitignore 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