Methods for analyzing next-generation sequencing data23. Metagenomic analysis (Part 2)

Abstract

Amplicon sequencing is a method of analyzing 16S ribosomal RNA (16S rRNA) nucleotide sequence information in all bacterial genomes. By amplifying the target sequence, it is possible to determine the phylogenetic composition of the bacteria present in a small sample. We first describe the primers used in the PCR and the general framework of the data analysis. We then describe the experimental design of the dataset and the installation of the R package dada2. Finally, we describe the R functions for string manipulation needed to handle the input and output files.