The oligotyping and minimum entropy decomposition (MED) pipeline for the analysis of marker gene amplicons
Oligotyping is a novel supervised computational method to decompose very closely related taxa within microbial communities by utilizing very subtle nucleotide variation among 16S Ribosomal RNA gene amplicon reads. It can reveal previously unobserved ecological patterns, and hidden diversity concealed within environmental datasets.
With oligotyping, depending on the hyper-variable region, similarity threshold between different types can be as low as 0.2%, more than a magnitude lower than de facto 3% similarity threshold that is being used by OTU clustering methods.
For installation and usage instructions, please see the project web page:
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