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Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform.

Andy Kilianski1, Patrick Carcel2, Shijie Yao3,4

  • 1Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. andrew.kilianski.ctr@mail.mil.

BMC Bioinformatics
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Summary
This summary is machine-generated.

Pathosphere, an open-source cloud tool, enhances pathogen detection using next-generation sequencing (NGS) by enabling collaborative bioinformatics pipelines. It successfully identified diverse pathogens and adapted to new analytical software for improved detection capabilities.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Pathogen Discovery

Background:

  • Next-generation sequencing (NGS) has advanced pathogen detection but lacks uniform analytical support.
  • Pathosphere.org is a cloud-based, open-source platform for sharing NGS analytical tools and data.
  • It facilitates collaboration among scientists in academia, industry, and government, eliminating the need for local hardware.

Purpose of the Study:

  • To evaluate the pathogen detection capabilities of the Pathosphere platform.
  • To demonstrate the utility and adaptability of Pathosphere for various NGS technologies.
  • To showcase the collaborative and open-source nature of the platform for bioinformatics tool development.

Main Methods:

  • Pathosphere's analytical pipelines were used to analyze pathogen-containing samples sequenced by NGS.
  • Samples included spiked human samples and those with human and zoonotic host backgrounds.
  • The platform's adaptability was tested by integrating pipelines from different research institutions.

Main Results:

  • Pathosphere pipelines successfully identified spiked pathogens across multiple NGS platforms (454, Ion Torrent, Illumina).
  • The platform detected known pathogens like arenavirus, flavivirus, and coronavirus in human and animal samples.
  • An adapted pipeline successfully detected parvovirus, which initial analyses missed due to limited homology.

Conclusions:

  • Pathosphere is a valuable platform for pathogen detection in complex samples using diverse NGS technologies.
  • The platform's plug-in adaptability allows for the integration of new analytical software.
  • It fosters a collaborative environment for developing and sharing bioinformatics tools for pathogen surveillance.