Analysis of Metagenomic Data

Abstract

In this chapter, we first briefly introduce the background of next- generation sequencing metagenomics, including the special properties in this research field and the challenges for statistical analysis. A metagenomic study typically consists of sampling, filtering, DNA extraction, sequencing, binning, assembly, profiling and down-stream analysis. We describe the widely used sta- tistical methods in determining the sufficiency of a metagenomic sample size, or classifying metagenomic sequencing reads into taxonomic bins, or assessing the accuracy of metagenomic assembly. In addition, we outline the steps and statistical methods for correcting the systematic errors in metagenomic profiling. Last, statistical methods for metagenomic comparison are discussed, including both parametric and non-parametric methods for comparison among different groups of multiple samples. The multiple comparison problem is also simply discussed.