UnCoVar

UnCoVar implements a Snakemake workflow for transparent and robust SARS-CoV-2 variant calling and lineage assignment that assembles virus genomes from patient samples, identifies existing lineages, and provides high-resolution insights into individual mutations.

Key Features:

• Variant Calling and Lineage Assignment: Performs virus genome assembly from patient samples, identifies existing lineages, and provides high-resolution insights into individual mutations.
• Cross-Platform Evaluation: Includes the first comprehensive cross-platform evaluation and validation of in silico SARS-CoV-2 typing workflows using a dataset of 54 patient-derived samples sequenced with several different in vitro approaches on all relevant state-of-the-art sequencing platforms.
• Quality Control: Includes extensive quality control measures.
• Generalizability: Easily generalizable towards other viral pathogens and future pandemics.
• Reproducibility and Scalability: Implemented as a robust, production-grade reproducible Snakemake workflow designed for reproducibility and scalability.

Scientific Applications:

• SARS-CoV-2 Typing: Types SARS-CoV-2 samples obtained from patients or environmental surveillance.
• Virus Genome Assembly: Assembles virus genomes from patient-derived samples.
• Lineage Identification: Identifies existing SARS-CoV-2 lineages and characterizes variants of concern.
• Pandemic Response Blueprint: Serves as a blueprint for dealing with future pandemics through generalizable viral pathogen analysis.

Methodology:

UnCoVar is implemented as a Snakemake workflow. The evaluation relies on a dataset of 54 patient-derived samples sequenced with several different in vitro approaches on all relevant state-of-the-art sequencing platforms.