ViroConstrictor¶

ViroConstrictor is a pipeline designed to process raw FastQ data from amplicon-based sequencing experiments and generate a biologically correct consensus sequence of the sequenced 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 getting started for download and installation instructions, and please see the user guide page page for basic usage instructions.

ViroConstrictor is available under the AGPLv3 licence

Authors¶

Florian Zwagemaker
Dennis Schmitz
Karim Hajji
Annelies Kroneman

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