DUDes: a top-down taxonomic profiler for metagenomics

Vitor C PiroBernhard Y Renard


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


Jan 27, 2007·Genome Research·Daniel H HusonStephan C Schuster
Oct 19, 2007·Nature·Peter J TurnbaughJeffrey I Gordon
Jun 10, 2009·Bioinformatics·Heng Li1000 Genome Project Data Processing Subgroup
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 13, 2012·Nature Methods·Nicola SegataCurtis Huttenhower
Aug 10, 2012·PLoS Pathogens·Claudio U KöserSharon J Peacock
Sep 11, 2012·Briefings in Bioinformatics·Sharmila S MandeTarini Shankar Ghosh
Nov 30, 2012·Nucleic Acids Research·Dennis A BensonEric W Sayers
Apr 11, 2013·JAMA : the Journal of the American Medical Association·Nicholas J LomanM J Pallen
Nov 28, 2013·Nature Reviews. Genetics·W Florian Fricke, David A Rasko
Jan 9, 2014·Statistics in Medicine·Jelle J Goeman, Aldo Solari
Mar 4, 2014·Genome Biology·Derrick E Wood, Steven L Salzberg
Apr 17, 2014·PLoS Medicine·Ingeborg KlymiukChristoph Steininger
Nov 16, 2014·Nucleic Acids Research·NCBI Resource Coordinators
Dec 17, 2014·Nucleic Acids Research·Ryszard KierzekElzbieta Kierzek
Feb 3, 2015·PloS One·Martin S Lindner, Bernhard Y Renard
May 23, 2015·Science·Shinichi SunagawaPeer Bork
Sep 30, 2015·Nature Methods·Duy Tin TruongNicola Segata
Jan 19, 2016·Scientific Reports·Stinus LindgreenPaul P Gardner


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

High-Throughput Nucleotide Sequencing
Trees (plant)
Research Study
Molecular Profiling
Top (Position)

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Systemic Juvenile Idiopathic Arthritis

Systemic juvenile idiopathic arthritis is a rare rheumatic disease that affects children. Symptoms include joint pain, but also fevers and skin rashes. Here is the latest on this disease.

Chromatin Regulation and Circadian Clocks

The circadian clock plays an important role in regulating transcriptional dynamics through changes in chromatin folding and remodelling. Discover the latest research on Chromatin Regulation and Circadian Clocks here.

Central Pontine Myelinolysis

Central Pontine Myelinolysis is a neurologic disorder caused most frequently by rapid correction of hyponatremia and is characterized by demyelination that affects the central portion of the base of the pons. Here is the latest research on this disease.

Myocardial Stunning

Myocardial stunning is a mechanical dysfunction that persists after reperfusion of previously ischemic tissue in the absence of irreversible damage including myocardial necrosis. Here is the latest research.

Pontocerebellar Hypoplasia

Pontocerebellar hypoplasias are a group of neurodegenerative autosomal recessive disorders with prenatal onset, atrophy or hypoplasia of the cerebellum, hypoplasia of the ventral pons, microcephaly, variable neocortical atrophy and severe mental and motor impairments. Here is the latest research on pontocerebellar hypoplasia.

Cell Atlas Along the Gut-Brain Axis

Profiling cells along the gut-brain axis at the single cell level will provide unique information for each cell type, a three-dimensional map of how cell types work together to form tissues, and insights into how changes in the map underlie health and disease of the GI system and its crosstalk with the brain. Disocver the latest research on single cell analysis of the gut-brain axis here.

Chronic Traumatic Encephalopathy

Chronic Traumatic Encephalopathy (CTE) is a progressive degenerative disease that occurs in individuals that suffer repetitive brain trauma. Discover the latest research on traumatic encephalopathy here.