PLACNETw

PLACNETw reconstructs plasmids from paired-end next-generation sequencing datasets by building and analyzing scaffold and homology graphs to separate plasmid contigs from chromosomal sequences.

Key Features:

• Graph-Based Reconstruction: Constructs graphs with two node types—contigs assembled from sequencing data and reference genomes—and two edge types representing scaffold links between contigs and homology to reference sequences.
• BLAST Automation: Automates BLAST searches to assess homology between contigs and reference genomes for graph annotation.
• Graph Pruning and Plasmid Extraction: Prunes the scaffold/homology graph to obtain connected component subgraphs representing individual plasmids.
• Paired-End NGS Input: Uses contigs derived from paired-end next-generation sequencing datasets as the basis for graph construction and analysis.

Scientific Applications:

• Microbial Genomics: Reconstruction of plasmids from bacterial genomes to identify and characterize plasmid sequences.
• Antibiotic Resistance and Pathogenicity Studies: Detection and characterization of plasmids involved in antibiotic resistance and pathogenicity.
• Horizontal Gene Transfer Research: Analysis of plasmid-mediated horizontal gene transfer among bacteria.

Methodology:

Builds graphs with contig and reference-genome nodes and scaffold-link and homology edges, automates BLAST homology searches, and prunes graphs to extract connected component subgraphs corresponding to plasmids.