Amplicon Sequencing(16S/18S/ITS)

Amplicon (16S/18S/ITS) sequencing with Illumina is a method of analyzing microbial diversity by identifying microbial profiles according to their sequences and then attempting to decipher community richness and diversity within each sample and between samples. The BMKCloud Amplicon (NGS) pipeline allows the analysis of 16S, 18S, ITS and multiple functional genes. It starts with read trimming, paired-end read assembly and quality assessment, followed by clustering of similar reads to generate Operational Taxonomic Units (OTUs) used in six different analysis sections. Taxonomic annotation provides information on the relative abundance and composition of each sample, while alpha and beta diversity analyses focus on microbial diversity within and between samples, respectively. Differential analysis between groups finds OTUs that differ using both parametric and non-parametric tests, while correlation analysis relates these differences to environmental factors. Finally, functional gene abundance is predicted based on marker gene abundance, providing insight into function and ecology in each sample..