├── .dockerignore ├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── LOG ├── README.md └── qiime2logfile.txt ├── README.md ├── README0.md ├── _README.md ├── _config.yml ├── _index.md ├── code ├── 00_allDemo_data.bash ├── 00_checkFiles_driver.bash ├── 01_metadataProfiling_driver.bash ├── 02_readPreprocess_driver.bash ├── 03_imapClassifySEQ_driver.bash ├── 04_1_phylotype_driver.bash ├── 04_2_otucluster_driver.bash ├── 04_3_phylogeny_driver.bash ├── README.md ├── Rmd │ ├── LatexsessionInfo.txt │ ├── README.Rmd.md │ ├── README.md │ ├── Rpackages.RData │ ├── clustering.Rmd │ ├── finalReport.Rmd │ ├── functions.RData │ ├── globalSetup.RData │ ├── global_setup.Rmd │ ├── global_setup.html │ ├── packages.RData │ ├── phylotype_constaxonomy_transformed.Rmd │ ├── report1.Rmd │ ├── report2.Rmd │ ├── report3.Rmd │ ├── report3.html │ ├── report4.Rmd │ ├── report4.html │ └── sessionInfo.txt ├── css │ ├── changelog.css │ └── report.css ├── dataFiles │ └── 01_get_demo_data.bash ├── dataanalysis │ ├── 01_phylotype_analysis.batch │ ├── 02_otus_analysis.batch │ ├── 03_phylogeny_analysis.batch │ └── iMAP_dataanalysis_driver.bash ├── datatransformation.bash ├── dockerImages.sh ├── iMAP_chunks_driver.sh ├── imapOTUanalysisReport_driver.bash ├── otutaxonomy │ ├── 01_get_shared_phylotype.batch │ ├── 02_get_shared_otus.batch │ ├── 03_get_shared_phylogeny_taxonomy.batch │ ├── 04_processed_seqs.bash │ ├── README.md │ └── iMAP_otutaxonomy_driver.bash ├── preprocessing │ ├── 01_install_preprocessing_software.bash │ ├── 02_get_read_statistics.bash │ ├── 03_get_basecall_scores.bash │ ├── 04_get_highscore_reads.bash │ ├── 05_get_qcphix_reads.bash │ ├── 06_final_seqkit.bash │ └── iMAP_preprocessing_driver.bash ├── progressreport1.bash ├── progressreport2.bash ├── progressreport3.bash ├── progressreport4.bash ├── qiime2 │ ├── README │ ├── convertmothur_biom.bash │ ├── qiime2-99-515-806-nb-classifier.bash │ ├── qiime2.bash │ └── qiime2_gg_classifier_fulllength.bash ├── refdatabase │ ├── 01_download_refDBs.bash │ ├── 02_download_ref_alignments.bash │ ├── 03_download_taxonomy_classifiers.bash │ └── iMAP_download_driver.bash ├── requirements │ ├── 00_get_raw_data.bash │ ├── 01_install_bbmap_software.bash │ ├── 01_install_linux_software.bash │ ├── 01_install_mac_software.bash │ ├── 02_download_ref_alignments.bash │ ├── 03_download_taxonomy_classifiers.bash │ ├── 04_check_folders_and_files.bash │ ├── iMAP_additional_software_driver.bash │ ├── iMAP_checkFiles_driver.bash │ ├── iMAP_requirements_linux_driver.bash │ └── iMAP_requirements_mac_driver.bash ├── seqclassification │ ├── 00_download_taxonoy_references.bash │ ├── 01_classify_seqs.batch │ └── iMAP_seqclassification_driver.bash ├── seqerrorrate │ ├── 00_get_mock_groups.batch │ ├── 01_calculate_error_rate.batch │ └── iMAP_seqerrorrate_driver.bash ├── seqprocessing │ ├── 01_assemble_paired_reads.batch │ ├── 02_align_for_16S_consensus.batch │ ├── 03_denoise_alignments.batch │ ├── 04_remove_chimeras.batch │ ├── README.md │ └── iMAP_seqprocessing_driver.bash ├── splitlefse.pl └── summarizeFastQC │ ├── 01_multiqc_fastqc_summary.bash │ ├── README.md │ └── iMAP_multiqc_driver.bash ├── data ├── metadata │ ├── README.md │ ├── bushmeat_2022_manifext.txt │ └── samplemetadata.tsv ├── mothur │ └── README.md ├── qiime2 │ └── README.md ├── raw │ └── README.md └── references │ └── README.md ├── defaultsettings.Rmd ├── docs └── index.html ├── iMAPMetadata.xlsx ├── imapmaterial.Rmd ├── img ├── README ├── filefolderstructure.png ├── iMAP-workflow.pdf ├── iMAP-workflow.png ├── otuabund.png ├── phyloclusters.png ├── qc0_fastQC.png ├── qced_fastQC.png ├── qctrim25_fastQC.png ├── qiime2view.png ├── required.png ├── structureOfiMAP.png └── structureOfiMAP2.png ├── library └── imap.bib ├── posters ├── README.md └── imapWorkflow.pdf ├── reports ├── README.md └── library │ └── imap.bib ├── resources ├── bbmap.zip ├── metadata │ ├── 186samples.metadata │ ├── README.md │ ├── bushmeat_2022_manifext.txt │ ├── manifest.txt │ ├── 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