├── IMNGS.md ├── LICENSE ├── MAG-pipeline.md ├── PICRUSt ├── README.md ├── iMGMC-16SrRNA-alignment.fasta ├── iMGMC-CopyNr-16SrRNA.tab ├── iMGMC-KO_traits.tab ├── iMGMC-MAGs16SrRNAlinks.tab ├── iMGMC-PICRUSt.bash ├── picrust-workflow-default.png └── picrust-workflow-denovo.png ├── README.md ├── creation-cataloge-pipeline.md ├── download.md ├── evaluation └── README.md ├── genecatalog-pipeline.md ├── images ├── Prevalence-Abundance-IMNGS.png ├── Taxonomy_Barplots_TaxLevels.png ├── iMGMC-creation-pipeline.png ├── logo-imngs.png ├── logo.png ├── pipeline.png ├── sMAG-creation-pipeline.png └── tutorials.png ├── linking ├── MetaData.csv ├── README.md ├── bash_file_workflow.sh ├── blast-matrix.txt ├── evaluation-tree.png ├── evaluation.md ├── forCor-16S-unambignousMappedReadsbyLibrary.txt ├── forCor-Bins-TPMbyLibrary.txt ├── linking.png ├── make-16S-mapping-stats.sh ├── make-bin-mapping-stats.sh ├── make-splitmapping-stats.sh ├── map-unambignous-matrix.txt ├── metaBin_16S_correlation_sq.R ├── meta_16S_corr.R ├── reformat-blast-results.sh └── workflow_management_16S_meta_int.R ├── sMAG-pipeline.md ├── scripts ├── download.sh ├── make-GeneID-ContigID-BinId-TPM-fromTPM.sh ├── make-GeneID-TPM-fromCovStats.sh ├── make-KO-TPM-fromTPM.sh ├── makeTPMfromCovStats.sh ├── makeTPMstats.sh ├── mapReadByBBmap.sh ├── splitTPMtoKeggKO.sh ├── splitTPMtoMGS.sh ├── splitTPMtoTaxonomy.sh ├── sumup-TPM-ContigID-BinID-files.sh ├── sumup-TPM-KOsum-files.sh ├── sumup-TPM-for-TaxLevels-fromContigTPM.sh ├── sumup-TPM-for-TaxLevels-fromTPM.sh └── translate-16S-to-MAGs.sh └── tutorials ├── data ├── MetaDATA-PRJNA390686.txt ├── Rscript_heatmap.R ├── Rscript_ordination.R ├── abundances-PRJNA390686-withTaxonomy.txt ├── abundances-PRJNA390686.txt ├── download-list-PRJNA390686.txt ├── headmap_abundances_Helicobacter.pdf └── headmap_abundances_mean.pdf ├── images ├── coverm-PRJNA390686-reformat.png ├── coverm-PRJNA390686.png ├── coverm.png ├── headmap_abundances_helicobacter.png ├── 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