MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Area of Science:

• Bacterial genomics
• Plasmid biology
• Bioinformatics tools

Background:

• Short-read sequencing is common for bacterial genetics, but plasmid analysis is challenging due to assembly issues.
• Plasmids vary in number and contain repetitive elements, complicating assembly and analysis.
• Existing plasmid analysis tools have variable performance and functionality.

Purpose of the Study:

• To develop and evaluate MOB-suite, a set of modular tools for plasmid reconstruction and typing from draft assembly data.
• To improve the characterization of plasmids in large-scale bacterial population studies.
• To provide enhanced plasmid typing including relaxase and conjugation potential.

Main Methods:

• MOB-suite was developed using Python 3.
• Performance was evaluated using closed bacterial genomes with publicly available Illumina data.
• Comparison with existing tools like plasmidfinder and plasmidSPAdes was conducted on a dataset of 377 known plasmids.

Main Results:

• MOB-suite identified plasmid contigs with 95% sensitivity and 88% specificity.
• MOB-suite accurately reconstructed 207 plasmids, compared to 102 by plasmidSPAdes, with fewer merge events.
• MOB-suite provides comprehensive typing, including relaxase and conjugation potential, surpassing plasmidfinder's capabilities.

Conclusions:

• MOB-suite is a sensitive and specific tool for bacterial plasmid reconstruction and typing.
• It outperforms existing tools in accurately assembling individual plasmids and reducing errors.
• MOB-suite facilitates detailed plasmid characterization, aiding bacterial population genetics studies.