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Published on: October 15, 2019
micropan: an R-package for microbial pan-genomics
Lars Snipen1, Kristian Hovde Liland2,3
1Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås, Norway. lars.snipen@nmbu.no.
This study introduces an R package designed for analyzing prokaryotic pan-genomes, facilitating the exploration of microbial diversity and strain-specific genes. The package aids in building computational pipelines for pan-genome studies.
Area of Science:
- Microbiology
- Bioinformatics
Background:
- A pan-genome encompasses all unique gene families within a prokaryotic species, often exceeding the size of a single genome due to high microbial diversity.
- Pan-genome studies are increasingly popular with accessible prokaryotic whole-genome sequence data.
- These studies reveal species diversity and identify genes crucial for bacterial survival or strain discrimination.
Purpose of the Study:
- To present a novel R package for the comprehensive study of prokaryotic pan-genomes.
- To provide a user-friendly tool for analyzing microbial diversity and gene families.
Main Methods:
- Development of an R package integrating statistical analyses and graphics capabilities.
- Utilization of external free software for intensive computational tasks.
- Functions provided for constructing a complete computational pipeline for pan-genome analysis.
Main Results:
- An R package is introduced for prokaryotic pan-genome research.
- The package leverages the R computing environment for advanced statistical analysis and visualization.
- It incorporates external software for demanding computations and offers pipeline-building functions.
Conclusions:
- The R package's utility is demonstrated using data from the bacterium Enterococcus faecalis.
- The package is freely available for download and installation from The Comprehensive R Archive Network (CRAN).
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