title: Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.
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.
authors.affiliation: 1​The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: Silvia
authors.initials: S
authors.lastname: Argimón
authors.affiliation: 1​The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: Khalil
authors.initials: K
authors.lastname: Abudahab
authors.affiliation: 1​The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: Richard J E
authors.initials: RJE
authors.lastname: Goater
authors.affiliation: 2​Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK.
authors.forename: Artemij
authors.initials: A
authors.lastname: Fedosejev
authors.affiliation: 1​The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: Jyothish
authors.initials: J
authors.lastname: Bhai
authors.affiliation: 1​The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: Corinna
authors.initials: C
authors.lastname: Glasner
authors.affiliation: 3​The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Feil
authors.affiliation: 4​School of Medicine, University of St. Andrews, St. Andrew, UK.
authors.forename: Matthew T G
authors.initials: MTG
authors.lastname: Holden
authors.affiliation: 1​The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.|2​Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK.
authors.forename: Corin A
authors.initials: CA
authors.lastname: Yeats
authors.affiliation: 5​Department of Infection Prevention and Hospital Hygiene, University Medical Centre Freiburg, Freiburg, Germany.
authors.forename: Hajo
authors.initials: H
authors.lastname: Grundmann
authors.affiliation: 2​Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK.
authors.forename: Brian G
authors.initials: BG
authors.lastname: Spratt
authors.affiliation: 1​The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.|2​Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK.
authors.forename: David M
authors.initials: DM
authors.lastname: Aanensen
mesh_terms: D023281:Genomics; D033181:Information Dissemination / Q000379:methods*; D020407:Internet; D008828:Microbiological Techniques / Q000379:methods*; D017720:Molecular Epidemiology / Q000379:methods*; D058974:Phylogeography / Q000379:methods*; D012984:Software
keywords: Open data; phylogenomics; phylogeography; population genomics; trees