Methods for analyzing next-generation sequencing data24. Metagenomic analysis (Part 3)

Abstract

The R package dada2 is an amplicon analysis program that takes metagenome read data as input and returns what strains are present in the sample. We describe a series of steps from quality control to taxonomic assignment of microbial mock community read data using R functions provided in the package. It is very easy to perform data analysis with R. It is not only in this package that it is important for the user to proceed with a correct understanding of the relationships between input and output. This paper contains many explanations of basic R functions (dim, length, sum, table, etc.). Even a good combination of these functions can confirm the results of the analysis from different perspectives.