Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
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Section: New Software and Platforms


Yet Another Pipeline for OTU building

Keywords: Taxonomies - Distance matrices - Clustering - Metagenomics

Functional Description: OTU building is one of the key operation in metabarcoding: how to delimit Operational Taxonomic Units in the "soup" where all amplicons of thousands of unicellular organisms have been lumped together (from visible plankton to nano- and picoplankton, for example). Yapotu is a software tool that enables approaches to unsupervised clustering on very large matrices of distances: each element is a distance between two reads produced by a sequencer. It permits one to select one method among several, like building MultiDimensional Scaling to produce an Euclidean image, and clustering within the point cloud, or building a graph where a node is a sequence and there is an edge if both sequences are at a distance smaller than a given threshold, and then after build connected components or communities on this graph. Other functions visualize the OTUs as clusters or subgraphs.