title: DUDes: a top-down taxonomic profiler for metagenomics.
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 Bioinformatics online.
  
  
  
  renardB@rki.de.
authors.affiliation: Research Group Bioinformatics (NG4), Robert Koch Institute, Nordufer 20, Berlin 13353, Germany CAPES Foundation, Ministry of Education of Brazil, Brasília - DF, 70040-020 Brazil.
authors.forename: Vitor C
authors.initials: VC
authors.lastname: Piro
authors.affiliation: Research Group Bioinformatics (NG4), Robert Koch Institute, Nordufer 20, Berlin 13353, Germany 4-Antibody AG, Hochberger Strasse 60C, Basel 4057, Switzerland.
authors.forename: Martin S
authors.initials: MS
authors.lastname: Lindner
authors.affiliation: Research Group Bioinformatics (NG4), Robert Koch Institute, Nordufer 20, Berlin 13353, Germany.
authors.forename: Bernhard Y
authors.initials: BY
authors.lastname: Renard
mesh_terms: D000465:Algorithms; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics