ViroConstrictor¶

ViroConstrictor is a pipeline designed to process raw FASTQ data from amplicon-based sequencing experiments and generate a biologically accurate consensus sequence of the sequenced genome.

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

ViroConstrictor can run on both standalone (Linux) computers and high-performance computing (HPC) infrastructures.

ViroConstrictor is compatible with Nanopore, Illumina, and IonTorrent data (FASTQ).

Please see the getting started page for download and installation instructions, and refer to the user guide page for basic usage instructions.

ViroConstrictor is available under the AGPLv3 licence.

Authors¶

Florian Zwagemaker
Dennis Schmitz
Karim Hajji
Gino Raaijmakers
Iveta Krskova
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