simurg: simulate bacterial pangenomes in R.
Bioinformatics
; 36(4): 1273-1274, 2020 02 15.
Article
in En
| MEDLINE
| ID: mdl-31584605
ABSTRACT
MOTIVATION 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. RESULTS:
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. AVAILABILITY AND IMPLEMENTATION The simurg package is released under the GPL-3 license, and is freely available for download from GitHub (https//github.com/iferres/simurg). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Genome
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2020
Document type:
Article
Affiliation country:
Uruguay