OMACASE

an open-source standalone Python package to analyze optical mapping data, with de novo repeat motif detection and analysis capabilities

License

• GPL-3.0-or-later

Written in & for

• Python 3.8+

Requirements

• Python 3.8+
• Docker (only if running inside a Docker container)
• wkhtmltopdf for PDF print
  • Make sure X11 server has been started for PDF printing

Installation

• python3 -m pip install --user omacase

(Alternatively) Runninng inside a Docker container

• docker build .
• docker run {image ID} OR
• docker run ccneko/omacase (pending registrations)

Getting Started

Below are some simple instructions to help you start using OMACASE

Importing the package in Python

• import omacase

Reading BNX / CMAP input in custom Python script

• your_bnx = opmap.BNX(your_bnx_path)
• your_cmap = opmap.CMAP(your_cmap_path)

Publication

• Chung CYL, Chan TF. OMACASE: Optical Mapping Quality Control and Repeat Detection Software. (Manuscript in preparation)