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Roary: rapid large-scale prokaryote pan genome analysis
Andrew J Page1, Carla A Cummins1, Martin Hunt1
1Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge.
Bioinformatics (Oxford, England)
|July 23, 2015
Summary
Roary is a new software tool that quickly builds large-scale prokaryote pan genomes, identifying core and accessory genes. This enables detailed genetic analysis of thousands of samples on a desktop computer.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Prokaryote population sequencing studies generate large datasets.
- Analyzing these datasets provides insights into prokaryotic genome structure.
Purpose of the Study:
- To introduce Roary, a novel tool for rapid pan-genome construction.
- To enable large-scale pan-genome analysis of prokaryote isolates.
Main Methods:
- Roary is implemented in Perl.
- It identifies core and accessory genes within large datasets.
- The tool is designed for efficient processing on standard hardware.
Main Results:
- Roary rapidly builds large-scale pan genomes.
- It accurately identifies core and accessory genes.
- A pan genome of 1000 isolates can be generated in 4.5 hours on a single CPU.
Conclusions:
- Roary facilitates comprehensive pan-genome analysis of thousands of prokaryote samples.
- The tool offers a balance of speed, accuracy, and accessibility.
- It is suitable for use on standard desktop computers.
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