An Open-source Quality Control Monitoring System for Clinical NGS
Project description
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.
ChronQC workflow
Examples:
ChronQC plots can be generated from,
- A custom SQLite database.
For example see, examples/custom_db_example.
- 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.
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
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for chronqc-1.0.1-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 330678a5926f100aeff33ce81c0da60903ebb423c9690e5d95f499379b5e7d00 |
|
MD5 | 15981bcba4614d6a1bdc335842765070 |
|
BLAKE2b-256 | 443eeac529c0443ac9b699d7738a1dff0393a4953e84b8c878f02340f5ceeee5 |