PCNE

PCNE estimates plasmid copy numbers from short-read sequencing data and assembled genomes.

Key Features:

• Input flexibility: PCNE accepts standard input data including raw reads and a genome assembly.
• Normalization strategy: PCNE applies a flexible normalization strategy for copy number estimation.
• GC-bias correction: PCNE includes an optional GC-bias correction step.
• Pipeline integration: PCNE is designed to complement existing plasmid detection pipelines.

Scientific Applications:

• Plasmid biology: PCNE enables deeper insights into plasmid biology through standardized copy number estimation.
• Antimicrobial resistance studies: PCNE supports research on antimicrobial resistance by quantifying plasmid copy numbers.
• Horizontal gene transfer studies: PCNE aids investigations of horizontal gene transfer by providing plasmid copy number estimates.

Methodology:

PCNE integrates state-of-the-art methodologies and applies a flexible normalization strategy with optional GC-bias correction to estimate plasmid copy numbers from raw reads and genome assemblies.