In the USEARCH-based ITS pipeline, R1 and R2 raw reads are processed by removing the primer sequences using Cutadapt v1.14 and then merged with USEARCH v.10. De-novo UPARSE-OTU algorithm is used to pick the OTUs at 97% of similarity and to remove chimeras. OTUs are identified against UNITE database version December 2017, collected in the .biom file and filtered at 0,005% abundance (Bokulich NA, et al., 2013) to eliminate spurious OTUs that are present at low frequency.
We deliver an archive via the cloud storage provider Mega. The most important file in the folder is an .html file that links to an interactive web page with sunburst, pie charts per sample and links for taxonomy table and .fastq reads download. An example of the output is available here.
When to use it
You should use such method when you need to analyze various matrices. Moreover, as it is a de-novo OTU-picking strategy, it can be applied to find new OTUs.