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A platform for leveraging next generation sequencing for routine microbiology and public health use

Citation

Rusu, LI and Wyres, KL and Reumann, M and Queiroz, C and Bojovschi, A and Conway, T and Garg, S and Edwards, DJ and Hogg, G and Holt, KE, A platform for leveraging next generation sequencing for routine microbiology and public health use, Health Information Science and Systems, 3, (S7) pp. 1-7. ISSN 2047-2501 (2015) [Refereed Article]


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Copyright Statement

Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) http://creativecommons.org/licenses/by/4.0/

Official URL: http://www.hissjournal.com/content/3/S1/S7

DOI: doi:10.1186/2047-2501-3-S1-S7

Abstract

Even with the advent of next-generation sequencing (NGS) technologies which have revolutionised the field of bacterial genomics in recent years, a major barrier still exists to the implementation of NGS for routine microbiological use (in public health and clinical microbiology laboratories). Such routine use would make a big difference to investigations of pathogen transmission and prevention/control of (sometimes lethal) infections. The inherent complexity and high frequency of data analyses on very large sets of bacterial DNA sequence data, the ability to ensure data provenance and automatically track and log all analyses for audit purposes, the need for quick and accurate results, together with an essential user-friendly interface for regular non-technical laboratory staff, are all critical requirements for routine use in a public health setting. There are currently no systems to answer positively to all these requirements, in an integrated manner. In this paper, we describe a system for sequence analysis and interpretation that is highly automated and tackles the issues raised earlier, and that is designed for use in diagnostic laboratories by healthcare workers with no specialist bioinformatics knowledge.

Item Details

Item Type:Refereed Article
Keywords:NGS, public health
Research Division:Information and Computing Sciences
Research Group:Information Systems
Research Field:Decision Support and Group Support Systems
Objective Division:Information and Communication Services
Objective Group:Computer Software and Services
Objective Field:Application Tools and System Utilities
Author:Garg, S (Dr Saurabh Garg)
ID Code:98692
Year Published:2015
Web of Science® Times Cited:2
Deposited By:Computing and Information Systems
Deposited On:2015-02-25
Last Modified:2015-04-09
Downloads:182 View Download Statistics

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