Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
By S. Argimón, K. AbuDahab, Richard J. Goater, Artemij Fedosejev, Jyothish Bhai, C. Glasner, E. Feil, M. Holden, C. Yeats, H. Grundmann and 2 more. Microbial Genomics, 2016
720 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/99d837a9c330f094ceb96983f4d1a12e17bed0bb
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In Molecular Biology
Citations in the corpus
- GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens (2017, neutral): “…were unable to even depict this large number of items, including PHYLOViZ 2.0 (Nascimento et al. 2017), SplitsTree4 (Huson and Bryant 2006), EvolView (He et al. 2016), Microreact (Argimon et al. 2016), TreeDyn (Chevenet et al. 2006), TreeView (Page 1996), and Phandango (Hadfield et al. 2018).”
- Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread (2019, methodology): “The phylogenetic tree was visualized together with associated metadata using Microreact [51].”
- Fast and flexible bacterial genomic epidemiology with PopPUNK (2018, methodology): “To enable interactive visualisation of these outputs, PopPUNK can write files formatted for Microreact (Argimón et al. 2016) , Phandango (Hadfield et al. 2017) and GrapeTree (Zhou et al. 2017) .”
- Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations (2023, neutral): “Existing tools such as NextStrain21 and frameworks such as Microreact22 primarily rely on a phylogeny to elucidate transmission chains and monitor the evolution of the virus.”