HaVoC

HaVoC performs reference-based consensus assembly and lineage assignment of SARS-CoV-2 sequences for variant surveillance.

Key Features:

• Reference-Based Consensus Assembly: Performs reference-based consensus assembly of raw SARS-CoV-2 sequencing reads to reconstruct viral genomes.
• Lineage Assignment: Assigns SARS-CoV-2 lineages to assembled genomes, enabling identification of variants of concern such as B.1.1.7, B.1.351, and P.1.
• Integration of Multiple Bioinformatic Tools: Leverages a suite of bioinformatic tools to perform comprehensive analyses on SARS-CoV-2 sequence data.
• Analysis of Genetic Variation: Facilitates investigation of genetic variance among SARS-CoV-2 samples for studying viral evolution and transmission.

Scientific Applications:

• Surveillance: Supports genomic surveillance of SARS-CoV-2 by producing consensus genomes and lineage calls for monitoring circulating strains.
• Variant Detection and Monitoring: Enables detection and tracking of variants of concern, including B.1.1.7, B.1.351, and P.1.
• Epidemiological Studies: Provides assembled genomes and lineage information for epidemiological analyses of transmission and outbreak dynamics.
• Public Health Genomics: Applied in national-level public health efforts such as surveillance and outbreak response (example: Finland).

Methodology:

Performs reference-based consensus assembly and lineage assignment by leveraging an integrated suite of bioinformatic tools.