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