The source data and codes related to the manuscript "Characterization of the pig lower respiratory tract antibiotic resistome".
The scripts of metagenomic analysis including the construction of the gene catalog and metagenome-assembled genomes are available at GitHub (https://github.com/Jingquan-Li/PRGC).
ARG_MGE_VFG.sh: Annotation of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors genes (VFGs).
ARGs_host_contigs.sh: Identification of ARG host bacteria based on contigs.
MAG_abudance.sh: The calculation of MAG abundances
Statistical analysis and visualization: Source data and code of statistical analysis and visualization.
Other_Figures_data.xlsx: The source data of figures plotted in Excel.