plassembler

plassembler assembles bacterial plasmid sequences from long-read and short-read sequencing data using a hybrid, long-read-first assembly approach with short-read polishing and chromosomal read removal to improve plasmid assembly accuracy and computational efficiency.

Key Features:

• Hybrid assembly: Performs a long-read-first assembly followed by short-read polishing to produce complete plasmid assemblies.
• Chromosomal read removal: Removes chromosomal reads from input datasets via a mapping approach to restrict assembly input to plasmid-specific reads and reduce misassembly.
• Plasmid–chromosome discrimination: Distinguishes plasmid sequences from chromosomal sequences to enhance assembly accuracy.
• Computational efficiency: Optimizes computational resources during plasmid assembly.
• Implementation: Implemented in Python.

Scientific Applications:

• Bacterial genetics: Enables reconstruction of bacterial plasmids for genetic and genomic studies.
• Antibiotic resistance gene mapping: Supports mapping and characterization of antibiotic resistance genes located on plasmids.
• Mobile genetic element characterization: Facilitates identification and analysis of mobile genetic elements carried on plasmids.
• Reproducible genomic analyses: Reduces manual curation to support reproducibility in plasmid-focused genomic studies.

Methodology:

Chromosomal reads are removed by mapping to isolate plasmid reads, followed by a long-read-first hybrid assembly with subsequent short-read polishing.