README_pypi.rst

ChronQC: A Quality Control Monitoring System for Clinical Next Generation Sequencing

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

ChronQC is a quality control (QC) tracking system for clinical implementation of next-generation sequencing (NGS). ChronQC generates time series plots for various QC metrics, which allows comparison of the current run to historical runs. ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds, and historical observations within a specified period. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping.

Features

• Suited for different assays in a clinical laboratory
• Generates interactive time series plots for various metrics
• Records users' notes and corrective actions onto the graphs to facilitate long-term recordkeeping
• Provides high level of customization: works with local databases and generates different chart types
• Leverages existing standard tools such as MultiQC

Example live ChronQC report

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

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

ChronQC is implemented in Python (tested with v2.7 / v3.5 / v3.6) and runs on all common operating systems (Windows, Linux and Mac OS X).

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

License

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