In the standard BMR pipeline, R1 and R2 raw reads are merged with FLASH software v.1.2.11 and quality filtered (Q>30). Reference-based UCLUST algorithm is used to pick the OTUs at 97% of similarity. OTUs are identified against Greengenes database v.13_8, 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 human-derived matrices. In fact, as it is a closed-reference system, it cannot be applied to find new OTUs, besides those present in the reference database (Greengenes).