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

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.