Metadata-Version: 2.4
Name: ViroConstrictor
Version: 1.6.6
Summary: Analysis of (targeted) Viral NGS data
Project-URL: homepage, https://rivm-bioinformatics.github.io/ViroConstrictor/
Project-URL: source-code, https://github.com/RIVM-bioinformatics/ViroConstrictor
Author: Florian Zwagemaker, Karim Hajji, Gino Raaijmakers, Dennis Schmitz, Margo Raijmakers, Annelies Kroneman
Author-email: ids-bioinformatics@rivm.nl
License-Expression: AGPL-3.0
License-File: LICENSE
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Affero General Public License v3
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Requires-Dist: aminoextract==0.4.1
Requires-Dist: biopython==1.85.*
Requires-Dist: biovalid==0.3.0
Requires-Dist: drmaa==0.7.9
Requires-Dist: fpdf2==2.8.4
Requires-Dist: openpyxl==3.1.5
Requires-Dist: pandas==2.3.3
Requires-Dist: pyyaml==6.0.3
Requires-Dist: rich==13.9.4
Requires-Dist: urllib3==2.5.0
Description-Content-Type: text/markdown

# ViroConstrictor

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/viroconstrictor/README.html)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7688035.svg)](https://doi.org/10.5281/zenodo.7688035)

[![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/RIVM-bioinformatics/ViroConstrictor?include_prereleases)](https://github.com/RIVM-bioinformatics/ViroConstrictor/releases/latest)
[![Conda](https://img.shields.io/conda/v/bioconda/viroconstrictor)](https://anaconda.org/bioconda/viroconstrictor)  
[![GitHub](https://img.shields.io/github/license/RIVM-bioinformatics/ViroConstrictor)](https://github.com/RIVM-bioinformatics/ViroConstrictor/blob/main/LICENSE)
[![CodeFactor](https://www.codefactor.io/repository/github/rivm-bioinformatics/viroconstrictor/badge)](https://www.codefactor.io/repository/github/rivm-bioinformatics/viroconstrictor)  
![GitHub deployments](https://img.shields.io/github/deployments/RIVM-bioinformatics/ViroConstrictor/github-pages?label=Documentation%20deployment)  



ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate  biologically correct consensus sequences from your data based on a given reference genome.

ViroConstrictor performs high speed data quality control, data cleanup and high accuracy removal of primer-sequences from NGS reads. As well as alignment of reads and generation of a consensus sequence using the TrueConsense consensus-caller which accounts for sequencing errors and alignment artefacts.

ViroConstrictor is able to run both on a standalone (linux) computer, as well as High-Performance Computing (HPC) infrastructures. 

ViroConstrictor is compatible with Nanopore, Illumina, and IONTorrent data (fastq).

Please see [the documentation](https://rivm-bioinformatics.github.io/ViroConstrictor/) for more information.

ViroConstrictor is available under the [AGPLv3 licence](https://www.gnu.org/licenses/agpl-3.0.en.html)

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If you use ViroConstrictor in your work, please cite:
> Zwagemaker, F., Hajji, K., Raaijmakers, G., Schmitz, D., Raijmakers, M., Kršková, I., Kroneman, A., & The RIVM-IDS Bioinformatics team. ViroConstrictor [Computer software]. https://doi.org/10.5281/zenodo.7688035 