Nam-Phuong Nguyen1, Siavash Mirarab1, Bo Liu1, Mihai Pop1, Tandy Warnow2. 1. Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA. 2. Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA.
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.
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.
Authors: Kevin Liu; Tandy J Warnow; Mark T Holder; Serita M Nelesen; Jiaye Yu; Alexandros P Stamatakis; C Randal Linder Journal: Syst Biol Date: 2011-12-01 Impact factor: 15.683
Authors: Prachi Kulkarni; Nathan D Olson; Joseph N Paulson; Mihai Pop; Cynthia Maddox; Emma Claye; Rachel E Rosenberg Goldstein; Manan Sharma; Shawn G Gibbs; Emmanuel F Mongodin; Amy R Sapkota Journal: Sci Total Environ Date: 2018-05-26 Impact factor: 7.963
Authors: Alexander Sczyrba; Peter Hofmann; Peter Belmann; David Koslicki; Stefan Janssen; Johannes Dröge; Ivan Gregor; Stephan Majda; Jessika Fiedler; Eik Dahms; Andreas Bremges; Adrian Fritz; Ruben Garrido-Oter; Tue Sparholt Jørgensen; Nicole Shapiro; Philip D Blood; Alexey Gurevich; Yang Bai; Dmitrij Turaev; Matthew Z DeMaere; Rayan Chikhi; Niranjan Nagarajan; Christopher Quince; Fernando Meyer; Monika Balvočiūtė; Lars Hestbjerg Hansen; Søren J Sørensen; Burton K H Chia; Bertrand Denis; Jeff L Froula; Zhong Wang; Robert Egan; Dongwan Don Kang; Jeffrey J Cook; Charles Deltel; Michael Beckstette; Claire Lemaitre; Pierre Peterlongo; Guillaume Rizk; Dominique Lavenier; Yu-Wei Wu; Steven W Singer; Chirag Jain; Marc Strous; Heiner Klingenberg; Peter Meinicke; Michael D Barton; Thomas Lingner; Hsin-Hung Lin; Yu-Chieh Liao; Genivaldo Gueiros Z Silva; Daniel A Cuevas; Robert A Edwards; Surya Saha; Vitor C Piro; Bernhard Y Renard; Mihai Pop; Hans-Peter Klenk; Markus Göker; Nikos C Kyrpides; Tanja Woyke; Julia A Vorholt; Paul Schulze-Lefert; Edward M Rubin; Aaron E Darling; Thomas Rattei; Alice C McHardy Journal: Nat Methods Date: 2017-10-02 Impact factor: 28.547
Authors: Christopher C M Baker; Leonora S Bittleston; Jon G Sanders; Naomi E Pierce Journal: Philos Trans R Soc Lond B Biol Sci Date: 2016-09-05 Impact factor: 6.237