DUDes: a top-down taxonomic profiler for metagenomics

Bioinformatics
Vitor C PiroBernhard Y Renard

Abstract

Species identification and quantification are common tasks in metagenomics and pathogen detection studies. The most recent techniques are built on mapping the sequenced reads against a reference database (e.g. whole genomes, marker genes, proteins) followed by application-dependent analysis steps. Although these methods have been proven to be useful in many scenarios, there is still room for improvement in species and strain level detection, mainly for low abundant organisms. We propose a new method: DUDes, a reference-based taxonomic profiler that introduces a novel top-down approach to analyze metagenomic Next-generation sequencing (NGS) samples. Rather than predicting an organism presence in the sample based only on relative abundances, DUDes first identifies possible candidates by comparing the strength of the read mapping in each node of the taxonomic tree in an iterative manner. Instead of using the lowest common ancestor we propose a new approach: the deepest uncommon descendent. We showed in experiments that DUDes works for single and multiple organisms and can identify low abundant taxonomic groups with high precision. DUDes is open source and it is available at http://sf.net/p/dudes Supplementary data are available at...Continue Reading

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Citations

Oct 13, 2016·Frontiers in Microbiology·María-Eugenia DeCastroMaría-Isabel González-Siso
Oct 3, 2017·Nature Methods·Alexander SczyrbaAlice C McHardy
Aug 10, 2017·Nature Reviews. Gastroenterology & Hepatology·Marcus J ClaessonPaul W O'Toole
Dec 19, 2019·Briefings in Bioinformatics·Richa Bharti, Dominik G Grimm
Oct 14, 2017·Briefings in Bioinformatics·Florian P BreitwieserSteven L Salzberg
Dec 11, 2019·Science Progress·Alexander Wy ChanHerb E Schellhorn
May 14, 2020·BMC Bioinformatics·Mikang SimJaebum Kim
Aug 16, 2017·Microbiome·Vitor C PiroBernhard Y Renard
May 10, 2018·Frontiers in Microbiology·Sam NooijMarion P G Koopmans
Nov 14, 2018·Bioinformatics·Temesgen Hailemariam DadiKnut Reinert
Apr 4, 2017·PeerJ·Temesgen Hailemariam DadiKnut Reinert
Aug 23, 2020·Genes·Quang Tran, Vinhthuy Phan
Mar 6, 2019·Genome Biology·Fernando MeyerDavid Koslicki

Related Concepts

Genome
Metagenomics
High-Throughput Nucleotide Sequencing
Genome
Trees (plant)
Research Study
Analysis
Molecular Profiling
Top (Position)
Species

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