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. 2016 Nov 30;2(11):e000093.
doi: 10.1099/mgen.0.000093. eCollection 2016 Nov.

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Silvia Argimón  1 , Khalil Abudahab  1 , Richard J E Goater  1 , Artemij Fedosejev  2 , Jyothish Bhai  1 , Corinna Glasner  1 , Edward J Feil  3 , Matthew T G Holden  4 , Corin A Yeats  1   2 , Hajo Grundmann  5 , Brian G Spratt  2 , David M Aanensen  1   2
Affiliations

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Silvia Argimón et al. Microb Genom. .

Abstract

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.

Keywords: Open data; phylogenomics; phylogeography; population genomics; trees.

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Figures

Fig. 1.
Fig. 1.
The Microreact workflow: input files (A); upload options (B, C and D); web application (E); map view (F); tree view (G); timeline (H); menu buttons to control bottom panel view (I), from left to right: timeline, view, table, info.
Fig. 2.
Fig. 2.
Visualization of local and global transmission events on Microreact. (a) Local, intra-species transmission of C. difficile visualized as closely related isolates from different sources sharing location and antibiotic phenotype. The bottom view panel shows the source selected as a colour filter for map and tree, and the streptomycin phenotype selected as a tree label. (b) Inter-continental transmission of Salmonella enterica serovar Typhi evidenced by the presence of closely related strains from Asia and Africa within the H58 clade. The country was selected as a colour filter for the map and tree, and the bottom table panel shows examples of closely related samples from Kenya and India.
Fig. 3.
Fig. 3.
Visualization of Campylobacter data from the NCBI Pathogen Detection Project linked live via the Microreact API. The data points are automatically grouped on the timeline. The visualization reflects the 4238 Campylobacter spp. genomes available as of 16th November 2016.
See this image and copyright information in PMC

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