publication . Preprint . Article . Other literature type . Conference object . Book . Part of book or chapter of book . 2017

Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

Zhemin Zhou; Nina Luhmann; Nabil-Fareed Alikhan; Christopher Quince; Mark Achtman;
Open Access English
  • Published: 07 Nov 2017
  • Publisher: Cold Spring Harbor Laboratory
  • Country: United Kingdom
Abstract
<jats:title>Abstract</jats:title><jats:p>Exploring the genetic diversity of microbes within the environment through metagenomic sequencing first requires classifying these reads into taxonomic groups. Current methods compare these sequencing data with existing biased and limited reference databases. Several recent evaluation studies demonstrate that current methods either lack sufficient sensitivity for species-level assignments or suffer from false positives, overestimating the number of species in the metagenome. Both are especially problematic for the identification of low-abundance microbial species, e. g. detecting pathogens in ancient metagenomic samples. ...
Subjects
free text keywords: Taxonomic rank, Biology, Data mining, computer.software_genre, computer, Data structure, Statistical model, Bioinformatics, Metagenomics, False positive paradox, Genetic diversity, Genome, Genetics, Computational biology, QH426, QR
Funded by
WT| Deep evolutionary history of bacterial pathogens
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 202792
  • Funding stream: Genetics, Genomics and Population Research
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