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

Chrispin Chaguza, Gerry Tonkin-Hill, Stephanie W Lo, James Hadfield, Nicholas J Croucher, Simon R Harris, Stephen D Bentley

Research output: Contribution to journalArticlepeer-review

4 Citations (SciVal)

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.

Original languageEnglish
Pages (from-to)1450-1451
Number of pages2
JournalBioinformatics
Volume38
Issue number5
Early online date2 Dec 2021
DOIs
Publication statusPublished - 1 Mar 2022

Bibliographical note

Funding
This work was supported by the Joint Initiative for Antimicrobial Resistance [MR/R003076/1]; the Bill and Melinda Gates Foundation [OPP1034556]; and Wellcome Trust [2016-2021 core award Grant 206194].

Data availability
All data are incorporated into the article and its online supplementary material.

Keywords

  • Genomics
  • Software
  • Genome
  • Bacteria
  • Biological Evolution

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