Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

Workflow Overview

Highlights

• Using state of the art tools, easily extended for other viruses

• Tool and database updates for critical components via Conda

• Built using modern design patterns with Conda and Snakemake

• Extensible and easy to customize

• Submission Ready Genomes

• Customizable reporting with comprehensive visualization

Four different example elements of the results generated by UnCoVar:

• a: The genome coverage of the aligned reads, visualized for multiple samples

• b: evaluation of known protein alterations from VOCs for one sample

• c: a pileup of reads at the position of one protein alteration. The mutations observed for multiple reads (grey bars) for a single sample, here in the S gene

• d: The lineage assignments inferred for single reads for one sample