/OMACASE

an open-source (GPLv3) standalone Python package to analyze optical mapping data, with de novo repeat motif detection and analysis capabilities

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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)