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RCandy: an R package for visualizing homologous recombinations in bacterial genomes.


ABSTRACT:

Summary

Homologous recombination is an important evolutionary process in bacteria and other prokaryotes, which increases genomic sequence diversity and can facilitate adaptation. Several methods and tools have been developed to detect genomic regions recently affected by recombination. Exploration and visualization of such recombination events can reveal valuable biological insights, but it remains challenging. Here, we present RCandy, a platform-independent R package for rapid, simple and flexible visualization of recombination events in bacterial genomes.

Availability and implementation

RCandy is an R package freely available for use under the MIT license. It is platform-independent and has been tested on Windows, Linux and MacOSX. The source code comes together with a detailed vignette available on GitHub at https://github.com/ChrispinChaguza/RCandy.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Chaguza C 

PROVIDER: S-EPMC8826011 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Publications

RCandy: an R package for visualizing homologous recombinations in bacterial genomes.

Chaguza Chrispin C   Tonkin-Hill Gerry G   Lo Stephanie W SW   Hadfield James J   Croucher Nicholas J NJ   Harris Simon R SR   Bentley Stephen D SD  

Bioinformatics (Oxford, England) 20220201 5


<h4>Summary</h4>Homologous recombination is an important evolutionary process in bacteria and other prokaryotes, which increases genomic sequence diversity and can facilitate adaptation. Several methods and tools have been developed to detect genomic regions recently affected by recombination. Exploration and visualization of such recombination events can reveal valuable biological insights, but it remains challenging. Here, we present RCandy, a platform-independent R package for rapid, simple a  ...[more]

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