Imperial College London
Alternate

Professor Neil Ferguson

Faculty of Medicine, School of Public Health

Director of the School of Public Health
 
 
 
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Contact

 

+44 (0)20 7594 3296neil.ferguson Website

 
 
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Location

 

508School of Public HealthWhite City Campus

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Summary

 

Publications

Citation

BibTex format

@article{Campbell:2018:10.1186/s12859-018-2330-z,
author = {Campbell, F and Didelot, X and Fitzjohn, R and Ferguson, N and Cori, A and Jombart, T},
doi = {10.1186/s12859-018-2330-z},
journal = {BMC Bioinformatics},
title = {outbreaker2: a modular platform for outbreak reconstruction},
url = {http://dx.doi.org/10.1186/s12859-018-2330-z},
volume = {19},
year = {2018}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Background:Reconstructing individual transmission events in an infectious disease outbreak can provide valuable information and help inform infection control policy. Recent years have seen considerable progress in the development of methodologies for reconstructing transmission chains using both epidemiological and genetic data. However, only a few of these methods have been implemented in software packages, and with little consideration for customisability and interoperability. Users are therefore limited to a small number of alternatives, incompatible tools with fixed functionality, or forced to develop their own algorithms at considerable personal effort.Results:Here we present outbreaker2, a flexible framework for outbreak reconstruction. This R package re-implements and extends the original model introduced with outbreaker, but most importantly also provides a modular platform allowing users to specify custom models within an optimised inferential framework. As a proof of concept, we implement the within-host evolutionary model introduced with TransPhylo, which is very distinct from the original genetic model in outbreaker, and demonstrate how even complex model results can be successfully included with minimal effort.Conclusions:outbreaker2provides a valuable starting point for future outbreak reconstruction tools, and represents a unifying platform that promotes customisability and interoperability. Implemented in the R software, outbreaker2joins a growing body of tools for outbreak analysis
AU  - Campbell,F
AU  - Didelot,X
AU  - Fitzjohn,R
AU  - Ferguson,N
AU  - Cori,A
AU  - Jombart,T
DO  - 10.1186/s12859-018-2330-z
PY  - 2018///
SN  - 1471-2105
TI  - outbreaker2: a modular platform for outbreak reconstruction
T2  - BMC Bioinformatics
UR  - http://dx.doi.org/10.1186/s12859-018-2330-z
UR  - http://hdl.handle.net/10044/1/59144
VL  - 19
ER  -
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