Introduction

MOTIVATION: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. RESULTS: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. AVAILABILITY: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat CONTACT: allen99@llnl.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. Scalable metagenomic taxonomy classification using a reference genome database.
    Cite this
    Ames SK, Hysom DA, Gardner SN, Lloyd GS, Gokhale MB, Allen JE, 2013-09-01 - Bioinformatics (Oxford, England)

Credits

  1. Sasha K Ames
    Developer

    Center for Applied Scientific Computing, Lawrence Livermore National Laboratory and Global Security Directorate, United States of America

  2. David A Hysom
    Developer

  3. Shea N Gardner
    Developer

  4. G Scott Lloyd
    Developer

  5. Maya B Gokhale
    Developer

  6. Jonathan E Allen
    Investigator

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Summary
AccessionBT006936
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByJonathan E Allen