A long-standing technique in metagenomics, particularly for those interested in bacterial microbiome studies, uses the sequencing of cloned copies (amplicons) of the 16S or 18S rRNA genes to create species profiles. These approaches can take advantage of lower throughput sequencing and the knowledge of the target sequence to classify each cloned sequence, simplifying the tricky task of assigning taxa to reads. In this recipe, we'll make use of the dada2 package to run an amplicon analysis from raw fastq sequence reads. We'll perform quality control and OTU assignment steps and use an interesting machine learning method to classify sequences.