Metagenomics (NGS)

Shotgun metagenomics with Illumina is a popular tool for studying microbiomes by directly sequencing DNA from complex samples, enabling the study of both taxonomic and functional diversity. The BMKCloud metagenomic (NGS) pipeline begins with quality control and metagenome assembly, from which genes are predicted and clustered into non-redundant datasets that are annotated for function and taxonomy using multiple databases. This information is used to analyze within-sample taxonomic diversity (alpha diversity) and between-sample diversity (beta diversity). Differential analysis between groups finds OTUs and biological functions that differ between the two groups using both parametric and non-parametric tests, while correlation analysis relates these differences to environmental factors.