Introduction

With the decrease in cost and increase in output of whole-genome shotgun technologies, many metagenomic studies are utilizing this approach in lieu of the more traditional 16S rRNA amplicon technique. Due to the large number of relatively short reads output from whole-genome shotgun technologies, there is a need for fast and accurate short-read OTU classifiers. While there are relatively fast and accurate algorithms available, such as MetaPhlAn, MetaPhyler, PhyloPythiaS, and PhymmBL, these algorithms still classify samples in a read-by-read fashion and so execution times can range from hours to days on large datasets. We introduce WGSQuikr, a reconstruction method which can compute a vector of taxonomic assignments and their proportions in the sample with remarkable speed and accuracy. We demonstrate on simulated data that WGSQuikr is typically more accurate and up to an order of magnitude faster than the aforementioned classification algorithms. We also verify the utility of WGSQuikr on real biological data in the form of a mock community. WGSQuikr is a Whole-Genome Shotgun QUadratic, Iterative, K-mer based Reconstruction method which extends the previously introduced 16S rRNA-based algorithm Quikr. A MATLAB implementation of WGSQuikr is available at: http://sourceforge.net/projects/wgsquikr.

Publications

  1. WGSQuikr: fast whole-genome shotgun metagenomic classification.
    Cite this
    Koslicki D, Foucart S, Rosen G, 2014-01-01 - PloS one

Credits

  1. David Koslicki
    Developer

    Mathematics Department, Oregon State University, United States of America

  2. Simon Foucart
    Developer

    Department of Mathematics, University of Georgia, United States of America

  3. Gail Rosen
    Investigator

    Department of Electrical and Computer Engineering, Drexel University, United States of America

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT000274
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByGail Rosen