MicroReset: characterization of the rabbit (Oryctolagus cuniculus) fecal metagenome and resistome by deep shotgun sequencing

Materials and Methods Data source This dataset was constructed using 30 rabbit fecal samples subjected to deep metagenomic sequencing. Data is published in the Bioproject PRJEB50625 Metagenomic assembly First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_000001635.27) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes by processing each sample separately (single-sample assembly). Contigs of less than 1500 bp were removed. MAGs recovery Reads of each sample were aligned against each assembly (30*30 mappings) with bowtie2 and results were indexed in sorted bam files with samtools. For each assembly, contigs coverage across all samples was computed with jgi_summarize_bam_contig_depths. MAGs were generated with MetaBAT 2 and SemiBin v1.3. MAGs quality was assessed with checkM and those with completeness 70% or contamination 5% or N50 8Kb were discarded.