├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── README.rst ├── bin └── refinem ├── refinem ├── VERSION ├── __init__.py ├── bin_comparer.py ├── cluster.py ├── common.py ├── coverage.py ├── data_files │ └── hmms │ │ ├── SSU_archaea.hmm │ │ ├── SSU_bacteria.hmm │ │ └── SSU_euk.hmm ├── deprecated │ └── taxonomic_profile.py ├── distributions │ ├── gc_dist.txt │ └── td_dist.txt ├── errors.py ├── genome_stats.py ├── main.py ├── outliers.py ├── plots │ ├── __init__.py │ ├── base_plot.py │ ├── combined_plots.py │ ├── cov_corr_plots.py │ ├── cov_perc_plots.py │ ├── distribution_plots.py │ ├── gc_cov_plot.py │ ├── gc_plots.py │ ├── mpld3_plugins.py │ ├── scatter.py │ ├── td_plots.py │ └── tetra_pca_plot.py ├── reference.py ├── scaffold_stats.py ├── ssu.py ├── taxon_profile.py ├── tetranucleotide.py ├── unbinned.py └── version.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- 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