The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform
Thomas C Matthews,
Franklin R Bristow,
Emma J Griffiths,
Geoffrey L Winsor,
Jennifer L. Gardy,
Patrick K.C. Tang,
The IRIDA Consortium João A Carriço,
Morag R Graham,
Andrew G McArthur,
Eduardo N Taboada,
Robert G. Beiko,
Fiona S.L. Brinkman,
William WL Hsiao,
Gary Van Domselaar
Posted 31 Jul 2018
bioRxiv DOI: 10.1101/381830
Posted 31 Jul 2018
Whole genome sequencing (WGS) is a powerful tool for public health infectious disease investigations owing to its higher resolution, greater efficiency, and cost-effectiveness over traditional genotyping methods. Implementation of WGS in routine public health microbiology laboratories is impeded by a lack of user-friendly automated and semi-automated pipelines, restrictive jurisdictional data sharing policies, and the proliferation of non-interoperable analytical and reporting systems. To address these issues, we developed the Integrated Rapid Infectious Disease Analysis (IRIDA) platform (irida.ca), a user-friendly, decentralized, open-source bioinformatics and analytical web platform to support real-time infectious disease outbreak investigations using WGS data. Instances can be independently installed on local high-performance computing infrastructure, enabling private and secure data management and analyses according to organizational policies and governance. IRIDA's data management capabilities enable secure upload, storage and sharing of all WGS data and metadata. The core platform currently includes pipelines for quality control, assembly, annotation, variant detection, phylogenetic analysis, in silico serotyping, multi-locus sequence typing, and genome distance calculation. Analysis pipeline results can be visualized within the platform through dynamic line lists and integrated phylogenomic clustering for research and discovery, and for enhancing decision-making support and hypothesis generation in epidemiological investigations. Communication and data exchange between instances are provided through customizable access controls. IRIDA complements centralized systems, empowering local analytics and visualizations for genomics-based microbial pathogen investigations. IRIDA is currently transforming the Canadian public health ecosystem and is freely available at https://github.com/phac-nml/irida and www.irida.ca.
- Downloaded 894 times
- Download rankings, all-time:
- Site-wide: 14,211 out of 92,330
- In bioinformatics: 2,220 out of 8,659
- Year to date:
- Site-wide: 21,770 out of 92,330
- Since beginning of last month:
- Site-wide: 20,134 out of 92,330
Downloads over time
Distribution of downloads per paper, site-wide
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!