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An Open-source Quality Control Monitoring System for Clinical NGS

Project description

https://github.com/nilesh-tawari/ChronQC/blob/master/docs/_static/ChronQC_logo.png https://readthedocs.org/projects/chronqc/badge/?version=latest

An Open-source Quality Control Monitoring System for Clinical NGS

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.

ChronQC workflow

https://github.com/nilesh-tawari/ChronQC/blob/master/docs/_static/ChronQC_workflow.png

Examples:

ChronQC plots can be generated from,

  1. A custom SQLite database.
  2. The output of MultiQC.

For complete command line reference see the documentation.

For details of chart types see the documentation.

Requirnment

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 using Conda from the Bioconda channel:

INSTALL_PATH=~/anaconda
wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
# or wget http://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh
bash Miniconda2-latest* -fbp $INSTALL_PATH
PATH=$INSTALL_PATH/bin:$PATH

conda update -y conda
conda config --add channels bioconda
conda install -c bioconda 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 preperation)

License

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

History

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

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