Sigma [electronic resource] : Strain-level inference of genomes from metagenomic analysis for biosurveillance

• Ngôn ngữ: eng
• Ký hiệu phân loại: 576.8 Evolution
• Thông tin xuất bản: Washington, D.C. : Oak Ridge, Tenn. : United States. Dept. of Energy. Office of Science ; Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy, 2014
• Mô tả vật lý: Size: p. 170-177 : , digital, PDF file.
• Bộ sưu tập: Metadata
• ID: 261344
• Chủ đề: 1. 59 basic biological sciences; 2. 60 applied life sciences

Tóm tắt

 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. In conclusion, 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.