Journal
MICROBIAL GENOMICS
Volume 5, Issue 4, Pages -Publisher
MICROBIOLOGY SOC
DOI: 10.1099/mgen.0.000220
Keywords
pangenome; microbial population genomics; machine learning; web application
Categories
Funding
- Centre for Genomic Pathogen Surveillance
- Wellcome Trust [099202, 104169/Z/14/Z]
- MRC [MR/N019296/1]
- ERC [742158]
- COIN Centre of Excellence
- NTD Modelling Consortium by the Bill & Melinda Gates Foundation
- Task Force for Global Health
- Royal Society [104169/Z/14/Z]
- NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
- Sir Henry Dale Fellowship
- MRC [MR/R015600/1, MR/N019296/1] Funding Source: UKRI
- Wellcome Trust [104169/Z/14/Z] Funding Source: Wellcome Trust
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The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here, we introduce PANINI (Pangenome Neighbour Identification for Bacterial Populations), a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding based on the t-SNE (t-distributed stochastic neighbour embedding) algorithm. PANINI is browser-based and integrates with the Microreact platform for rapid online visualization and exploration of both core and accessory genome evolutionary signals, together with relevant epidemiological, geographical, temporal and other metadata. Several case studies with single- and multi-clone pneumococcal populations are presented to demonstrate the ability to identify biologically important signals from gene content data. PANINI is available at http://panini.pathogen.watch and code at http://gitlab.com/cgps/panini.
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