Abstract
Motivation: Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. Results: We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP combines SAT\'e-enabled phylogenetic placement a phylogenetic placement method, with statistical techniques to control the classification precision and recall, and results in improved abundance profiles. TIPP is highly accurate even in the presence of high indel errors and novel genomes, and matches or improves on previous approaches, including NBC, mOTU, PhymmBL, MetaPhyler and MetaPhlAn.
Original language | English (US) |
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Pages (from-to) | 3548-3555 |
Number of pages | 8 |
Journal | Bioinformatics |
Volume | 30 |
Issue number | 24 |
DOIs | |
State | Published - Dec 15 2014 |
ASJC Scopus subject areas
- Statistics and Probability
- Biochemistry
- Molecular Biology
- Computer Science Applications
- Computational Theory and Mathematics
- Computational Mathematics
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Data for Taxonomic Identification and Phylogenetic Profiling
Nguyen, N.-P. (Creator), Mirarab, S. (Creator), Bo, L. (Creator), Pop, M. (Creator) & Warnow, T. (Creator), University of Illinois Urbana-Champaign, Oct 29 2014
DOI: 10.13012/B2IDB-8783447_V1
Dataset