OMTools

OMTools is a software tool that has been developed to process and visualize large-scale optical map data. Optical mapping is a molecular technique that captures specific patterns of fluorescent labels along DNA molecules. It has been widely applied in assisted scaffolding in sequence assemblies, microbial strain typing, and detection of structural variations. OMTools includes modules for visualization (OMView), data processing, and simulation. These modules form an accessible and convenient pipeline for optical mapping analyses.

The visualization module (OMView) lets users view and interact with large-scale optical mapping profiles. It provides an intuitive and user-friendly interface for exploring optical mapping data. Users can zoom in and out, pan and rotate the view, and adjust the display settings. The module also includes various tools for data analysis, such as peak detection, signal filtering, and data normalization.

The data processing module of OMTools enables users to preprocess optical mapping data and extract relevant features. It includes tools for profile alignment, data smoothing, and segmentation. The module supports various file formats, including OMB, BNX, and CMAP. The data processing module makes it easier for users to prepare their data for downstream analysis.

The simulation module of OMTools allows users to simulate optical mapping experiments and evaluate different experimental designs. It includes tools for generating synthetic optical mapping profiles, simulating labeling protocols, and evaluating the effect of experimental parameters on the resulting profiles. The simulation module is a valuable tool for optimizing experimental protocols and evaluating the performance of different optical mapping platforms.