HaVoC
HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences.

HAVoC (Helsinki university Analyzer for Variants Of Concern)
HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. HAVoC is a pipeline utilizing several bioinformatic tools to perform multiple necessary analyses for investigating genetic variance among SARS-CoV-2 samples.The pipeline is ideal for those who need a more accessible and fast tool to detect and monitor the spread of SARS-CoV-2 variants of concern during local outbreaks.
If using HAVoC, please cite :
Phuoc Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura (2021) HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences ( 2021) bioRxiv, https://doi.org/10.1101/2021.02.12.431018