Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

PanGIA: A Metagenomics Analytical Framework for Routine Biosurveillance and Clinical Pathogen Detection

Po-E Li, View ORCID ProfileJoseph A. Russell, David Yarmosh, Alan G. Shteyman, Kyle Parker, Hillary Wood, J.R. Aspinwall, Richard Winegar, Karen Davenport, Chien-chi Lo, John Bagnoli, Phillip Davis, Jonathan L. Jacobs, Patrick S.G. Chain
doi: https://doi.org/10.1101/2020.04.20.051813
Po-E Li
1Los Alamos National Laboratory, Los Alamos, NM, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joseph A. Russell
2MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joseph A. Russell
  • For correspondence: jrussell@mriglobal.org
David Yarmosh
2MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alan G. Shteyman
2MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kyle Parker
3MRIGlobal, 425 Volker Blvd, Kansas City, MO, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hillary Wood
3MRIGlobal, 425 Volker Blvd, Kansas City, MO, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J.R. Aspinwall
3MRIGlobal, 425 Volker Blvd, Kansas City, MO, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard Winegar
3MRIGlobal, 425 Volker Blvd, Kansas City, MO, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Karen Davenport
1Los Alamos National Laboratory, Los Alamos, NM, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chien-chi Lo
1Los Alamos National Laboratory, Los Alamos, NM, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John Bagnoli
2MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Phillip Davis
2MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jonathan L. Jacobs
2MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Patrick S.G. Chain
1Los Alamos National Laboratory, Los Alamos, NM, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

ABSTRACT

Metagenomics is emerging as an important tool in biosurveillance, public health, and clinical applications. However, ease-of-use for execution and data analysis remains a barrier-of-entry to the adoption of metagenomics in applied health and forensics settings. In addition, these venues often have more stringent requirements for reporting, accuracy, and precision than the traditional ecological research role of the technology. Here, we present PanGIA (Pan-Genomics for Infectious Agents), a novel bioinformatics analysis platform for hosting, processing, analyzing, and reporting shotgun metagenomics data of complex samples suspected of containing one or more pathogens. PanGIA was developed to address gaps that often preclude clinicians, medical technicians, forensics personnel, or other non-expert end-users from the routine application of metagenomics for pathogen identification. Though primarily designed to detect pathogenic microorganisms within clinical and environmental metagenomics data, PanGIA also serves as an analytical framework for microbial community profiling and comparative metagenomics. To provide statistical confidence in PanGIA’s taxonomic assignments, the system provides two independent estimations of probability for species and strain level detection. First, PanGIA integrates coverage data with ‘uniqueness’ information mapped across each reference genome for a stand-alone determination of confidence for each query sequence at each taxonomy level. Second, if a negative-control sample is provided, PanGIA compares this sample with a corresponding experimental unknown sample and determines a measure of confidence associated with ‘detection above background’. An integrated graphical user interface allows interactive interrogation and enables users to summarize multiple sample results by confidence score, normalized read abundance, reference genome linear coverage, depth-of-coverage, RPKM, and other metrics to detect specific organisms-of-interest. Comparison testing of the PanGIA algorithm against a number of recent k-mer, read-mapping, and marker-gene based taxonomy classifiers across various real-world datasets with spiked targets shows superior mean positive predictive value, sensitivity, and specificity. PanGIA can process a five million paired-end read dataset in under 1 hour on commodity computational hardware. The source code and documentation are publicly available at https://github.com/LANL-Bioinformatics/PanGIA or https://github.com/mriglobal/PanGIA. The database for PanGIA can be downloaded from ftp://bioinformatics.mriglobal.org/. The full GUI-based PanGIA analysis environment is available in a Docker container and can be installed from https://hub.docker.com/r/poeli/pangia/.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵† Formerly at MRIGlobal – now at QIAGEN Digital Insights A/S, Aarhus, Denmark

  • ↵ϕ Formerly at MRIGlobal – now at L3Harris Technologies, Inc.

  • ftp://bioinformatics.mriglobal.org/

  • https://github.com/LANL-Bioinformatics/PanGIA

  • https://hub.docker.com/r/poeli/pangia/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted April 23, 2020.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
PanGIA: A Metagenomics Analytical Framework for Routine Biosurveillance and Clinical Pathogen Detection
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
PanGIA: A Metagenomics Analytical Framework for Routine Biosurveillance and Clinical Pathogen Detection
Po-E Li, Joseph A. Russell, David Yarmosh, Alan G. Shteyman, Kyle Parker, Hillary Wood, J.R. Aspinwall, Richard Winegar, Karen Davenport, Chien-chi Lo, John Bagnoli, Phillip Davis, Jonathan L. Jacobs, Patrick S.G. Chain
bioRxiv 2020.04.20.051813; doi: https://doi.org/10.1101/2020.04.20.051813
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
PanGIA: A Metagenomics Analytical Framework for Routine Biosurveillance and Clinical Pathogen Detection
Po-E Li, Joseph A. Russell, David Yarmosh, Alan G. Shteyman, Kyle Parker, Hillary Wood, J.R. Aspinwall, Richard Winegar, Karen Davenport, Chien-chi Lo, John Bagnoli, Phillip Davis, Jonathan L. Jacobs, Patrick S.G. Chain
bioRxiv 2020.04.20.051813; doi: https://doi.org/10.1101/2020.04.20.051813

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3506)
  • Biochemistry (7348)
  • Bioengineering (5324)
  • Bioinformatics (20266)
  • Biophysics (10020)
  • Cancer Biology (7744)
  • Cell Biology (11306)
  • Clinical Trials (138)
  • Developmental Biology (6437)
  • Ecology (9954)
  • Epidemiology (2065)
  • Evolutionary Biology (13325)
  • Genetics (9361)
  • Genomics (12587)
  • Immunology (7702)
  • Microbiology (19027)
  • Molecular Biology (7444)
  • Neuroscience (41049)
  • Paleontology (300)
  • Pathology (1230)
  • Pharmacology and Toxicology (2138)
  • Physiology (3161)
  • Plant Biology (6861)
  • Scientific Communication and Education (1273)
  • Synthetic Biology (1897)
  • Systems Biology (5313)
  • Zoology (1089)