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TIPP: Taxon Identification and Phylogenetic Profiling

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Mathematical, Statistical and Computational Aspects of the New Science of Metagenomics

Co-authors: Nam Nguyen (UT-Austin), Siavash Mirarab (UT-Austin), Mihai Pop (University of Maryland, College Park), Bo Liu (University of Maryland, College Park)

Abundance profiling is a crucial step in understanding the diversity of a metagenomic sample. Key to estimating an accurate profile is the ability to perform taxonomic identification of the metagenomic reads. Many methods have been developed for taxonomic identification, however, the current best methods often fail to classify many fragments, especially at lower taxonomic levels.

We present TIPP (taxon identification and phylogenetic profiling), a new marker-based taxon identification and abundance profiling method. TIPP combines a highly accurate phylogenetic placement method (SEPP) with statistical techniques to control the precision and recall of the classification results. We show that TIPP is more robust to sequencing error and has better recall than other marker-based taxon identification methods. TIPP also yields highly accurate abundance profiles, matching or improving on many previous approaches, including NBC , PhymmBL, MetaPhyler, and MetaPhlAn.

This talk is part of the Isaac Newton Institute Seminar Series series.

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