Introduction

MOTIVATION: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. RESULTS: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic reads to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. The algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. AVAILABILITY AND IMPLEMENTATION: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. Sigma: strain-level inference of genomes from metagenomic analysis for biosurveillance.
    Cite this
    Ahn TH, Chai J, Pan C, 2015-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Tae-Hyuk Ahn
    Developer

    Computer Science and Mathematics Division, Oak Ridge National Laboratory, United States of America

  2. Juanjuan Chai
    Developer

    Computer Science and Mathematics Division, Oak Ridge National Laboratory, United States of America

  3. Chongle Pan
    Investigator

    Computer Science and Mathematics Division, Oak Ridge National Laboratory, United States of America

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Summary
AccessionBT006624
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByChongle Pan