Pathoscope 2.0.6 / Clinical PathoScope 1.0.4 – Species Identification and Strain Attribution with Unassembled Sequencing data

Pathoscope 2.0.6  / Clinical PathoScope 1.0.4


Pathoscope takes a next-generation sequencing reads from a mixture sample of multiple strains of genomes and it predicts which genomes potentially belongs there. Different from most of approach including composition method or similarity search with a daunting task of de novo assembly, the software applies the propagation of evidence in the Bayesian framework to an initial alignment result and reassign an correct membership of mapping by using the expectation and maximization algorithm.

Clinical Pathoscope is a program to identify pathogens/commensals/contaminants in unassembled sequencing reads.


W. Evan Johnson Lab




  • Linux


  Pathoscope / Clinical PathoScope



PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.
Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.
Microbiome. 2014 Sep 5;2:33. doi: 10.1186/2049-2618-2-33.

Genome Res. 2013 Oct;23(10):1721-9. doi: 10.1101/gr.150151.112.
Pathoscope: Species identification and strain attribution with unassembled sequencing data.
Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE.

BMC Bioinformatics. 2014 Aug 4;15:262. doi: 10.1186/1471-2105-15-262.
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.
Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA1, Johnson WE.