Comparison of Nanopore MinION and Illumina NovaSeq for metagenomic characterization of the human lower respiratory tract infection microbiome Metagenome
High-throughput sequencing is a critical tool in microbial community analysis, with next-generation sequencing (NGS) and third-generation sequencing (TGS) constituting the most widely used technologies. The taxonomic identification capabilities of NGS platforms (e.g., Illumina NovaSeq) compared to TGS platforms (e.g., Oxford Nanopore Technologies MinION) remain unclear. In the present study, we explored the microbial communities of infected lower respiratory tracts via high-depth and shallow metagenomic species detection with NGS and ONT, respectively.