SnakeLines workflow for SARS-CoV-2 variant detection from next-generation sequencing reads

The ongoing SARS-CoV-2 pandemic, which emerged in December 2019, revolutionized genomic surveillance, leading to new means of tracking viral spread and monitoring genetic changes in their genomes over time. One of the key sequencing methods used during the pandemic is based on massively parallel short read sequencing based on Illumina technology. In this work, we present a highly scalable and easily deployable computational pipeline for the analysis of Illumina sequencing data, which is used in Slovak SARS-CoV-2 genomic surveillance efforts. We discuss several issues that arose during the pipeline design, and which could both provide useful insight into the analysis processes and serve as a guideline for optimized future outbreak surveillance projects. Copyright © 2021 for this paper by its authors.