ViroConstrictor

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ViroConstrictor

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

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# ViroConstrictor

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

ViroConstrictor

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