Comparison of Illumina, ONT, and PacBio HiFi sequencing for gut metagenome characterization
Shotgun metagenomic sequencing was performed on gut microbiome samples from cattle, pig, and humandonor feces using three sequencing platforms: Illumina (paired-end 150 bp), Oxford NanoporeTechnologies (ONT), and PacBio HiFi. The objective was to evaluate how sequencing platform andassembly strategy affect the recovery of mobile genetic elements, plasmid-borne antimicrobialresistance genes, and metagenome-assembled genomes. Each sample was sequenced on all threeplatforms, yielding nine datasets. DNA was extracted using the Wizard HMW DNA Extraction Kit(Promega). Library preparation and sequencing were performed by CJ Bioscience Inc (Seoul, SouthKorea).