Rapid genotyping of targeted viral samples using Illumina short-read sequencing data

The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numerous datasets and showed that the consensus genome of samples could be obtained reliably without further manual data curation. Our pipeline can be a valuable tool for fast identifying viral samples. The pipeline is publicly available on the project's GitHub page (https://github.com/laczkol/QVG).

Automated summary

This paper introduces a pipeline for reconstructing the dominant consensus genome of viral samples and analyzing their within-host variability. Through benchmarking on multiple datasets, it is shown that the pipeline is reliable and can quickly identify viral samples.