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 for more information.
ViroConstrictor is available under the AGPLv3 licence
If you use ViroConstrictor in your work, please cite:
Zwagemaker, F., Hajji, K., Schmitz, D., Kroneman, A., & The RIVM-IDS Bioinformatics team. ViroConstrictor [Computer software]. https://doi.org/10.5281/zenodo.7688035