├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── RScripts ├── ContigCoverageVisualizer.Rmd ├── README.md ├── eggnog_management.Rmd ├── pileupVisualizer.R └── rsconnect │ └── documents │ └── ContigCoverageVisualizer.Rmd │ └── shinyapps.io │ └── redsnic │ └── ContigCoverageVisualizer.dcf ├── WGALP ├── __init__.py ├── blocks │ ├── BWA.py │ ├── FastQC.py │ ├── SPAdes.py │ ├── TrimmomaticPE.py │ ├── __init__.py │ ├── bamtools_stats.py │ ├── bazam.py │ ├── bracken.py │ ├── bwa_index.py │ ├── checkM.py │ ├── fastq_bam_difference.py │ ├── kraken.py │ ├── load_krakendb_ramdisk.py │ ├── mauve.py │ ├── merqury.py │ ├── minia.py │ ├── prokka.py │ ├── quast.py │ ├── r_node_analysis.py │ ├── recycler.py │ ├── samtools_VSI.py │ ├── samtools_depth.py │ ├── samtools_stats.py │ └── unload_krakendb_ramdisk.py ├── checkpoint.py ├── step.py ├── tools │ ├── __init__.py │ └── filter_fastq.py ├── utils │ ├── __init__.py │ ├── commandLauncher.py │ ├── genericUtils.py │ └── input_manager.py └── workflow.py ├── configure.sh ├── docker_bashrc.sh ├── fetch_example_data.sh ├── mini_programs ├── __init__.py ├── assemble_with.py ├── check_coverage.py ├── decontamination_workflow.py ├── eval_WGA_quality.py ├── evaluate_quality.py ├── filter_fasta.py ├── filter_fastq.py ├── kdb_load.py ├── kdb_unload.py ├── order_contigs.py ├── prokka_annotate.py ├── run_recycle.py ├── understand_origin.py └── view_nodes.py ├── other_scripts ├── clean_space_in_fasta.py ├── contamination_level_simulation.sh ├── eggnog_letterfreq.R ├── extract_gene_ids_by_presence_absence_roary.R ├── filter_pangenome.sh ├── filter_spades_nodes_by_coverage.py ├── get_kegg.R ├── install_merqury.sh ├── kraken_table.R ├── kraken_table.Rmd ├── prepare_simulations.sh └── test │ └── filtered_contigs.fasta ├── setup.py ├── simpleGUI └── decontaminationGUI.py ├── sub_workflows ├── __init__.py ├── compute_coverage.py ├── decontamination.py ├── extract_plasmids.py ├── fastq_trimming.py └── kraken_bracken.py └── wgalp.py 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