Microbiome Analysis Using 16S Amplicon Sequencing: From Samples to ASVs.

In this chapter, we will present an outline of a typical experimental and bioinformatic workflow for identification of bacterial amplicon sequence variants (ASVs) present in a set of samples. This chapter is written from a bioinformatic point of view; therefore, the specific experimental protocols are not detailed, but rather the impact of various experimental decisions on the downstream analysis is described. Emphasis is made on the transition from reads to ASVs, describing the Deblur algorithm.