Phase 2: OTU picking, classification and phylogenetic tree generation
During this phase reads are processed so that comparisons between samples can be made. The first step is to cluster reads based on similarity into OTUs and to select a representative sequence for each OTU. Each OTU is then classified by comparison to a reference database and a phylogeny inference is made based on sequence alignment and the construction of a phylogenetic tree.
Input: high quality reads
Output: OTUs, representative sequences, OTU table with classification and abundance of each OTU, heatmap, sequence alignment and phylogenetic tree
Bibliography
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