OMTools

OMTools processes and visualizes optical mapping data to extract fluorescent labels along DNA molecules for applications including assisted scaffolding of sequence assemblies, microbial strain typing, and detection of structural variations.

Key Features:

• OMView: Visualizes optical mapping data to display fluorescent-label patterns along DNA molecules.
• Data Processing Module: Processes optical mapping data to analyze and interpret captured fluorescent-label patterns.
• Simulation Module: Simulates optical mapping experiments and expected fluorescent-label patterns for validation and assessment.

Scientific Applications:

• Assisted scaffolding: Supports assisted scaffolding of sequence assemblies using optical mapping label patterns.
• Microbial strain typing: Enables typing of microbial strains based on optical mapping profiles.
• Structural variation detection: Detects structural variations via differences in fluorescent-label patterns along DNA molecules.

Methodology:

OMTools comprises modules for visualization (OMView), processing of fluorescent-label patterns, and simulation of optical mapping experiments; it is implemented in Java 1.8.