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PathSeq

Identifies non-human nucleic acids that reveal candidate microbes. PathSeq is a highly scalable software tool that provides computational subtraction of high throughput sequencing (HTS) data. This application demonstrates high sensitivity and specificity in its capacity to distinguish between human and non-human sequences using both simulated and experimental transcriptome data and entire genome sequencing data. It is implemented in a cloud computing environment, making it easily accessible to the scientific community.

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PathSeq forum

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PathSeq classification

  • Viruses

PathSeq specifications

Software type:
Pipeline/Workflow
Restrictions to use:
None
Programming languages:
Java, Python
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Parallelization:
MapReduce
Version:
2.0
High performance computing:
Yes

PathSeq distribution

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PathSeq support

Maintainer

  • Matthew Meyerson <>

Credits

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Publications

Institution(s)

Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA

Funding source(s)

Supported by the National Cancer Institute (RC2CA148317), the Starr Cancer Consortium, the Claudia Adams Barr Program in Innovative Cancer Research, a Natural Sciences and Engineering Research Council of Canada Postgraduate Scholarship, and the Rebecca Ridley Kry Fellowship of the Damon Runyon Cancer Research Foundation.

Link to literature

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