2-AIN-506, 2-AIN-252: Seminar in Bioinformatics (2), (4)
Summer 2026
Abstrakt

James Robertson, John H. E. Nash. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom, 4(8). 2018.

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Download from publisher: http://mgen.microbiologyresearch.org/pubmed/content/journal/mgen/10.1099/mgen.0.000206 PubMed

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Abstract:

Large-scale bacterial population genetics studies are now routine due to 
cost-effective Illumina short-read sequencing. However, analysing plasmid content 
remains difficult due to incomplete assembly of plasmids. Bacterial isolates can 
contain any number of plasmids and assembly remains complicated due to the 
presence of repetitive elements. Numerous tools have been developed to analyse 
plasmids but the performance and functionality of the tools are variable. The 
MOB-suite was developed as a set of modular tools for reconstruction and typing 
of plasmids from draft assembly data to facilitate characterization of plasmids. 
Using a set of closed genomes with publicly available Illumina data, the 
MOB-suite identified contigs of plasmid origin with both high sensitivity and 
specificity (95 and 88 %, respectively). In comparison, plasmidfinder 
demonstrated high specificity (99 %) but limited sensitivity (50 %). Using the 
same dataset of 377 known plasmids, MOB-recon accurately reconstructed 207 
plasmids so that they were assigned to a single grouping without other plasmid or 
chromosomal sequences, whereas plasmidSPAdes was only able to accurately 
reconstruct 102 plasmids. In general, plasmidSPAdes has a tendency to merge 
different plasmids together, with 208 plasmids undergoing merge events. The 
MOB-suite reduces the number of errors but produces more hybrid plasmids, with 84 
plasmids undergoing both splits and merges. The MOB-suite also provides replicon 
typing similar to plasmidfinder but with the inclusion of relaxase typing and 
prediction of conjugation potential. The MOB-suite is written in Python 3 and is 
available from https://github.com/phac-nml/mob-suite.