Pathoscope: species identification and strain attribution with unassembled sequencing data.

ABSTRACT: Emerging next-generation sequencing technologies have revolutionized the collection of genomic data for applications in bioforensics, biosurveillance, and for use in clinical settings. However, to make the most of these new data, new methodology needs to be developed that can accommodate large volumes of genetic data in a computationally efficient manner. We present a statistical framework to analyze raw next-generation sequence reads from purified or mixed environmental or targeted infected tissue samples for rapid species identification and strain attribution against a robust database of known biological agents. Our method, Pathoscope, capitalizes on a Bayesian statistical framework that accommodates information on sequence quality, mapping quality, and provides posterior probabilities o

SUBMITTER: Francis OE 

PROVIDER: S-EPMC3787268 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature