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 languageEnglish (US)
Pages (from-to)3548-3555
Number of pages8
JournalBioinformatics
Volume30
Issue number24
DOIs
StatePublished - Dec 15 2014

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Metagenomics
Phylogenetics
Profiling
Genes
Genome
Placement

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

TIPP : Taxonomic identification and phylogenetic profiling. / Nguyen, Nam Phuong; Mirarab, Siavash; Liu, Bo; Pop, Mihai; Warnow, Tandy.

In: Bioinformatics, Vol. 30, No. 24, 15.12.2014, p. 3548-3555.

Research output: Contribution to journalArticle

Nguyen, Nam Phuong ; Mirarab, Siavash ; Liu, Bo ; Pop, Mihai ; Warnow, Tandy. / TIPP : Taxonomic identification and phylogenetic profiling. In: Bioinformatics. 2014 ; Vol. 30, No. 24. pp. 3548-3555.
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