An Open-source Quality Control Monitoring System for Clinical NGS

• Free software: MIT license
• Documentation: http://chronqc.readthedocs.io/en/latest/.

Features

• Designed for quality control based on historical data
• Generates interactive time-series plots for various metrics, allowing comparison of the current run to historical runs
• Record users' notes and corrective actions directly onto the graphs for long-term record-keeping
• Provides highly customizable different chart types
• Supports customized database for plotting
• Works with output of MultiQC

ChronQC is an open-source, interactive, record-keeping QC system. ChronQC captures QC data from MultiQC. output and stores the metrics in a database. ChronQC then automatically generates interactive time-series plots for various metrics, allowing comparison of the current run to historical runs. In QC meetings, users can record their notes and corrective actions directly onto the graphs for long-term record-keeping.

Live report:

https://nilesh-tawari.github.io/chronqc

ChronQC workflow

Examples:

ChronQC plots can be generated from,

1. A custom SQLite database.

   • For example see, examples/custom_db_example.

2. The output of MultiQC.

   • For example on creating the ChronQC database and plots see, examples/multiqc_example_1.
   • For example on creating, updating the ChronQC database and plots see, examples/multiqc_example_2.

For complete command line reference see the documentation.

For details of chart types see the documentation.

Requirement

Generating database and creating interactive charts is performed with code written for Python.

Installation

You can install ChronQC from PyPI using pip as follows:

pip install chronqc

Alternatively, you can install from GitHub:

git clone https://github.com/nilesh-tawari/ChronQC.git
cd ChronQC
pip install -r requirements.txt
pip install --editable .

If you would like the development version instead, the command is:

pip install --upgrade --force-reinstall git+https://github.com/nilesh-tawari/ChronQC.git

Citation

An Open-source Quality Control Monitoring System for Clinical NGS (Manuscript under construction)

License

This project is licensed under the MIT License - see the LICENSE.md file for details