In the Amplicon-Based Analysis folder you will find all the tools needed to cluster reads at some level of similarity into pseudo-species called Operational Taxonomic Units (OTUs), where all reads within for example 97% similarity are clustered together and represented by a single sequence. To this effect, we recommend the use of workflows, where all the steps needed to cluster the reads in OTUs have been pre-organized and optimized to facilitate your analysis. These workflows are found in the Microbial Workflows folder inside the Amplicon-based OTU Clustering folder (see Amplicon-Based Analysis Workflows).
- Normalize OTU Table by Copy Number
- Filter Samples Based on Number of Reads
- OTU clustering
- Remove OTUs with Low Abundance
- Align OTUs with MUSCLE
- Amplicon-Based Analysis Workflows