Pathosphere.org

Pathogen detection and characterization through a web-based, open source informatics platform

Andy Kilianski, Patrick Carcel, Shijie Yao, Pierce Roth, Josh Schulte, Greg B. Donarum, Ed T. Fochler, Jessica M. Hill, Alvin T. Liem, Michael R Wiley, Jason T. Ladner, Bradley P. Pfeffer, Oliver Elliot, Alexandra Petrosov, Dereje D. Jima, Tyghe G. Vallard, Melanie C. Melendrez, Evan Skowronski, Phenix Lan Quan, W. Ian Lipkin & 4 others Henry S. Gibbons, David L. Hirschberg, Gustavo F. Palacios, C. Nicole Rosenzweig

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Background: The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. Results: The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. Conclusions: By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.

Original languageEnglish (US)
Article number416
JournalBMC Bioinformatics
Volume16
Issue number1
DOIs
StatePublished - Dec 29 2015
Externally publishedYes

Fingerprint

Informatics
Pathogens
Open Source
Web-based
Parvovirus
Pipelines
Sequencing
Arenavirus
Flavivirus
Coronavirus
Zoonoses
Computational Biology
Communicable Diseases
Biomedical Research
Industry
Software
Communication
Databases
Ions
Adaptability

ASJC Scopus subject areas

  • Applied Mathematics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

Kilianski, A., Carcel, P., Yao, S., Roth, P., Schulte, J., Donarum, G. B., ... Rosenzweig, C. N. (2015). Pathosphere.org: Pathogen detection and characterization through a web-based, open source informatics platform. BMC Bioinformatics, 16(1), [416]. https://doi.org/10.1186/s12859-015-0840-5

Pathosphere.org : Pathogen detection and characterization through a web-based, open source informatics platform. / Kilianski, Andy; Carcel, Patrick; Yao, Shijie; Roth, Pierce; Schulte, Josh; Donarum, Greg B.; Fochler, Ed T.; Hill, Jessica M.; Liem, Alvin T.; Wiley, Michael R; Ladner, Jason T.; Pfeffer, Bradley P.; Elliot, Oliver; Petrosov, Alexandra; Jima, Dereje D.; Vallard, Tyghe G.; Melendrez, Melanie C.; Skowronski, Evan; Quan, Phenix Lan; Lipkin, W. Ian; Gibbons, Henry S.; Hirschberg, David L.; Palacios, Gustavo F.; Rosenzweig, C. Nicole.

In: BMC Bioinformatics, Vol. 16, No. 1, 416, 29.12.2015.

Research output: Contribution to journalArticle

Kilianski, A, Carcel, P, Yao, S, Roth, P, Schulte, J, Donarum, GB, Fochler, ET, Hill, JM, Liem, AT, Wiley, MR, Ladner, JT, Pfeffer, BP, Elliot, O, Petrosov, A, Jima, DD, Vallard, TG, Melendrez, MC, Skowronski, E, Quan, PL, Lipkin, WI, Gibbons, HS, Hirschberg, DL, Palacios, GF & Rosenzweig, CN 2015, 'Pathosphere.org: Pathogen detection and characterization through a web-based, open source informatics platform', BMC Bioinformatics, vol. 16, no. 1, 416. https://doi.org/10.1186/s12859-015-0840-5
Kilianski, Andy ; Carcel, Patrick ; Yao, Shijie ; Roth, Pierce ; Schulte, Josh ; Donarum, Greg B. ; Fochler, Ed T. ; Hill, Jessica M. ; Liem, Alvin T. ; Wiley, Michael R ; Ladner, Jason T. ; Pfeffer, Bradley P. ; Elliot, Oliver ; Petrosov, Alexandra ; Jima, Dereje D. ; Vallard, Tyghe G. ; Melendrez, Melanie C. ; Skowronski, Evan ; Quan, Phenix Lan ; Lipkin, W. Ian ; Gibbons, Henry S. ; Hirschberg, David L. ; Palacios, Gustavo F. ; Rosenzweig, C. Nicole. / Pathosphere.org : Pathogen detection and characterization through a web-based, open source informatics platform. In: BMC Bioinformatics. 2015 ; Vol. 16, No. 1.
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AU - Donarum, Greg B.

AU - Fochler, Ed T.

AU - Hill, Jessica M.

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