├── LICENSE ├── Manual_MuDoGeR.md ├── README.md ├── conda_installation_and_usage.md ├── dependencies_description.md ├── flowcharts ├── figure_1_overview.jpg ├── module_1_ovrw.jpg ├── module_2_ovrw.jpg ├── module_3_ovrw.jpg ├── module_4_ovrw.jpg ├── module_5_ovrw.jpg └── mudoger_outputs.jpg ├── installation ├── .config_std.sh ├── MuDoGeR_default_parameters.sh ├── config.sh ├── config_bkp.sh ├── database-setup.sh ├── dependencies │ ├── BRAT-for-mudoger.py │ ├── README_anisplitter.md │ ├── aniSplitter.R │ ├── computeNullParameters.R │ ├── extract_fa.py │ ├── implementing_bootstrap.R │ ├── make_table_clusters.py │ ├── mdcheck.py │ ├── mpred_function_predict_memory.R │ ├── mpred_models.RData │ ├── mpred_predict.R │ ├── mudoger_singularity.sh │ ├── mudoger_singularity_slurm.sh │ ├── organize-bins-tax_and_filtern50.py │ ├── otupick_dependencies │ │ ├── aniSplitter.R │ │ ├── environment.yml │ │ ├── gOTUpick.sh │ │ ├── organize-bins-tax.py │ │ ├── pick_rep.R │ │ └── summarize-anisplitter-results.py │ ├── predict_mem_input-SLURM.sh │ ├── predict_mem_input.sh │ ├── split-all-seq.py │ ├── strain_differentiation_wf.sh │ ├── tpm_cov_table_mudoger.py │ ├── unique-kmers.py │ ├── unique_kmers.tsv │ └── vir_virfinder_script.r ├── genemark_maker2_installation.md ├── install.sh ├── installation_scripts │ ├── install_module_1.sh │ ├── install_module_2.sh │ ├── install_module_3.sh │ ├── install_module_4.sh │ └── install_module_5.sh └── installation_utils.sh ├── src ├── modules │ ├── mudoger-module-1.sh │ ├── mudoger-module-2.sh │ ├── mudoger-module-3.sh │ ├── mudoger-module-4.sh │ └── mudoger-module-5.sh ├── mudoger └── scripts │ ├── mudoger-module-1-1_QC.sh │ ├── mudoger-module-1-2_kmermempred.sh │ ├── mudoger-module-1-3_assembly.sh │ ├── mudoger-module-2-1_initial-binning.sh │ ├── mudoger-module-2-2_bin-ref-bacteria.sh │ ├── mudoger-module-2-3_bin-ref-archea.sh │ ├── mudoger-module-2-4_bin-dereplication.sh │ ├── mudoger-module-2-5_bin-taxonomy.sh │ ├── mudoger-module-2-6_bin-QC.sh │ ├── mudoger-module-2-7_prokka.sh │ ├── mudoger-module-2-8_genomics-metrics.sh │ ├── mudoger-module-3-1_viral-investigation.sh │ ├── mudoger-module-3-2_vcontact2.sh │ ├── mudoger-module-3-3_host-prediction.sh │ ├── mudoger-module-3-4_vcheck.sh │ ├── mudoger-module-3-5_uvigs-metrics.sh │ ├── mudoger-module-4-1_eukrep-eukbin-filter.sh │ ├── mudoger-module-4-2_genemark.sh │ ├── mudoger-module-4-3_eukcc.sh │ ├── mudoger-module-4-4_maker2.sh │ ├── mudoger-module-4-5_busco.sh │ ├── mudoger-module-5-1_prokOTUpicking.sh │ ├── mudoger-module-5-2-1_BRAT_pmags.sh │ ├── mudoger-module-5-2-2_BRAT_uvigs.sh │ ├── mudoger-module-5-2-3_BRAT_emabs.sh │ ├── mudoger-module-5-2_BRAT.sh │ └── mudoger-module-5-3_genemap.sh ├── traffic ├── clones.csv ├── plots.png └── views.csv └── understand_main_outputs.md /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdsufz/MuDoGeR/HEAD/LICENSE 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