Comparative Evaluation of Sequencing Platforms for Shotgun Metagenomics Surveys

Shotgun metagenomics approach was applied to a mock community, leveraging three distinct sequencing platforms to evaluate their performance and limitations. Using a commercially available prokaryotic mock community, we established a controlled benchmarking framework to assess sequencing accuracy, coverage and assembly efficiency. We examined the challenges associated with each sequencing protocol and assessed the ability of different assemblers to reconstruct high-quality MAGs. Additionally, microbial taxonomic assignment and functional predictions based on the recovered MAGs were also explored. Here, we provide a case test using standards characterized by intra- and inter-species diversity to highlight the pros and cons of the shotgun metagenomic approach, as well as the capabilities of the available technologies for exploring multiple aspects of the microbiome's dark matter.