Preface    ◾    xv

(demultiplexing and quality control), metagenomic feature processing (OTU clustering,

DADA2 denoising, Deblur denoising, and UNOISE2 denoising), taxonomy assignment

and construction of phylogenetic trees, microbial diversity analysis (alpha diversity and

beta diversity), and data analysis with QIIME2.

Chapter 8 discusses the shotgun metagenomic data analysis. The discussion includes

data acquisition, quality control, removal of host DNA, assembly-free taxonomic profil-

ing, assembly evaluation, de novo assembly of metagenomes, binning, bin evaluation, and

prediction of gene transcript and gene annotation.

The computer codes used in the book chapters and their updates will be available at

“https://github.com/hamiddi/ngs”.