Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores

• DOI: 10.1099/mgen.0.000398
• Publication Date: 2020-06-24T15:15:01Z
• Authors: Oliver Schwengers; Patrick Barth; Linda Falgenhauer; Torsten Hain; Trinad Chakraborty; Alexander Goesmann
• Keywords: Replicon

Plasmids are extrachromosomal genetic elements that replicate independently of the chromosome and play a vital role in environmental adaptation bacteria. Due to potential mobilization or conjugation capabilities, plasmids important vehicles for antimicrobial resistance genes virulence factors with huge increasing clinical implications. They therefore subject large genomic studies within scientific community worldwide. As result rapidly improving next-generation sequencing methods, quantity sequenced bacterial genomes is constantly increasing, turn raising need specialized tools (i) extract plasmid sequences from draft assemblies, (ii) derive their origin distribution, (iii) further investigate repertoire. Recently, several bioinformatic methods have emerged tackle this issue; however, combination high sensitivity specificity sequence identification rarely achieved taxon-independent manner. In addition, many software not appropriate high-throughput analyses cannot be included existing pipelines due technical design implementation. study, we investigated differences replicon distributions protein-coding on scale as new approach distinguish plasmid-borne chromosome-borne contigs. We defined computed statistical discrimination thresholds metric: distribution score (RDS), which an accuracy 96.6 %. The final performance was improved by RDS metric heuristics exploiting plasmid-specific higher-level contig characterizations. implemented workflow bioinformatics tool called Platon recruitment characterization contigs short-read assemblies. Compared PlasFlow, higher (97.5 %) more balanced predictions (F1=82.6 tested broad range taxa better equal against targeted PlasmidFinder PlaScope Escherichia coli isolates. available at: http://platon.computational.bio/ .