Gplas

Gplas reconstructs and partitions plasmid sequences from short-read whole-genome sequencing (WGS) data to enable analysis of plasmid structure and dissemination in bacterial populations.

Key Features:

• Plasmid Separation: Distinguishes and separates plasmid contigs into discrete components using sequence- and graph-based signals.
• Data Integration: Integrates sequence composition and coverage metrics with assembly graph information to improve plasmid binning accuracy.
• Network Partitioning: Applies network partitioning on pruned networks of plasmid unitigs to define discrete plasmid components.
• Scalability: Processes large collections of bacterial isolates to support high-throughput plasmid analyses.
• Workflow Management: Implements analysis steps with R and Bash scripts and is orchestrated via a Snakemake pipeline.

Scientific Applications:

• Epidemiological Studies: Traces dissemination of antibiotic resistance genes, for example the vanA gene cluster in Enterococcus faecium.
• Pairwise Isolate Comparisons: Compares predicted plasmids between isolates to assess potential epidemiological links.
• Discrimination of Transmission Modes: Helps distinguish clonal dissemination from horizontal gene transfer (HGT) in resistance gene spread.
• Outbreak Analysis: Identifies scenarios where plasmid-mediated dissemination contributes to outbreak dynamics.

Methodology:

Contig binning using sequence composition and coverage; refinement using assembly graph information; network partitioning of pruned plasmid unitig networks to produce discrete plasmid components; implemented with R and Bash scripts and managed by a Snakemake pipeline.