simurg: simulate bacterial pangenomes in R.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
15 02 2020
15 02 2020
Historique:
received:
19
03
2019
revised:
06
08
2019
accepted:
25
09
2019
pubmed:
5
10
2019
medline:
18
9
2020
entrez:
5
10
2019
Statut:
ppublish
Résumé
The pangenome concept describes genetic variability as the union of genes shared in a set of genomes and constitutes the current paradigm for comparative analysis of bacterial populations. However, there is a lack of tools to simulate pangenome variability and structure using defined evolutionary models. We developed simurg, an R package that allows to simulate bacterial pangenomes using different combinations of evolutionary constraints such as gene gain, gene loss and mutation rates. Our tool allows the straightforward and reproducible simulation of bacterial pangenomes using real sequence data, providing a valuable tool for benchmarking of pangenome software or comparing evolutionary hypotheses. The simurg package is released under the GPL-3 license, and is freely available for download from GitHub (https://github.com/iferres/simurg). Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 31584605
pii: 5581402
doi: 10.1093/bioinformatics/btz735
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1273-1274Informations de copyright
© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.