Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
Open accessAbstract
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.
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“The merged data were uploaded into the visualization tool Microreact [77] along with the phylogenetic trees for B. subtilis and B. velezensis .”
Self-citation
- Authors
- Argimón, S., Abudahab, K., Goater, R. J. E., Fedosejev, A., Bhai, J., Glasner, C., Feil, E. J., Holden, M. T. G., Yeats, C. A., Grundmann, H., Spratt, B. G., & Aanensen, D. M.
- Affiliations
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Imperial College London (GB)
- University of Bath (GB)
- University of St Andrews (GB)
- University Medical Center Freiburg (DE)
- Corresponding author
- Aanensen, David M.
- ORCID
- Venue
- Microbial Genomics
- Publisher
- Microbiology Society
- Published
- 2016-11-30
- Volume
- 2
- Issue
- 11
- Pages
- e000093-e000093
- ISSN
- 2057-5858 (ISSN-L)
- PMC
- PMC5320705
- OpenAlex
- W2560057613
- Cited by
- 732
- References
- 20
- Citations by year
- 2026: 55 · 2025: 81 · 2024: 102 · 2023: 95 · 2022: 100 · 2021: 129 · 2020: 81 · 2019: 45 · 2018: 33 · 2017: 8 · 2016: 2
- FWCI
- 19.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Microbial Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- St Andrews Research Repository (St Andrews Research Repository) (submittedVersion, cc-by)
- Spiral (Imperial College London) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (099202, 089472)
- National Institute for Health and Care Research (HPRU-2012-10080)
- Topics
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Data Visualization and Analytics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- phylogeography, genomic epidemiology, interactive data visualization, phylogenetic tree, web application, data sharing, metadata integration, interactive querying, data visualization tools
- MeSH terms
- Microbiological Techniques, Software, Molecular Epidemiology, Internet, Genomics, Information Dissemination, Phylogeography
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