title: Sigma: strain-level inference of genomes from metagenomic analysis for biosurveillance.
abstract: BACKGROUND
  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.
  
  
  METHODS
  Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Tae-Hyuk
authors.initials: TH
authors.lastname: Ahn
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Juanjuan
authors.initials: J
authors.lastname: Chai
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Chongle
authors.initials: C
authors.lastname: Pan
mesh_terms: D000465:Algorithms; D055877:Biosurveillance; D019295:Computational Biology / Q000379:methods*; D004269:DNA, Bacterial / Q000032:analysis*; D016680:Genome, Bacterial; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004269:DNA, Bacterial