Gut Microbiota and Resistome Profiles of Swiss Expatriates in Africa Revealed by Nanopore Metagenomics

This dataset contains the final metagenome-assembled genomes (MAGs), which were polished using 4 iterations of Racon and 1 iteration of Medaka, and were then used in the taxonomic (CheckM and GTDB-Tk), resistome (ResFinder) and plasmid (PlasmidFinder) analyses related to this project. The preprocessed Nanopore reads used to generate the MAGs are available in the NCBI SRA database under the BioProject number PRJNA1285875. It also contains intermediate analysis outputs (i.e. reports) from CheckM, GTDB-Tk, Kraken2, PlasmidFinder and ResFinder. The folder structure and its contents are as follows: CheckM/|-- CheckM_reports (contains individual CheckM reports; total 71 *.tsv files)|-- HQ-MAG-bins_post_CheckM (contains high-quality bins per sample: total 379 *.fa.gz files) GTDB-Tk/ Contains the GTDB-Tk taxonomy classification of the HQ-MAG-Bins_post_CheckM reports (2 files) Kraken2/|-- Kraken2_individual_reports (contains individual Kraken2 reports: total 72 *.kreport.gz files)|-- Kraken2_merged_reports (contains the merged Kraken2 report: 1 .tsv file) MAGs/ Contains all polished MAGs used in this study (contains 72 *.fasta.gz files) PlasmidFinder/|-- PlasmidFinder_individual_reports (contains individual PlasmidFinder screening reports: 72 *.tsv files)|-- PlasmidFinder_replicon_counts_table (contains the replicon sequence counts table: 1 .tsv file)`-- Plasmids_extracted_contigs_from_MAGs (contains MAG contigs associated with replicon sequences and ARGs: 33 *.fasta.gz files) ResFinder/|-- ARGs_gene_counts_table (contains the original ARG count table: 1 tsv.file)|-- ResFinder_individual_reports (contains individual ResFinder screening reports: 72 *.txt files)`-- ResFinder_PlasmidFinder_merged_report (contains a single merged report of samples associated with contigs containing both ARGs and replicon sequences)