#1Viralgenie, a Nextflow Pipeline for Viral Metagenome Sequencing Data: Application in LASV Research
Joon Klaps, Liana Kafetzopoulou, and Philippe Lemey
I present viralgenie, a Nextflow computational pipeline for processing viral metagenomic sequencing data. Viralgenie enables the identification of intrahost variants as well as the reconstruction of consensus genomes for segmented viruses using a combination of denovo and reference-based mapping. The pipeline is part of a larger project which focuses on the disease development of the Lassa virus. It is currently processing metagenome and hybridization capture-based sequencing data of diagnostic and longitudinal samples. In future research viralgenie’s results will be used to unravel Lassa’s intrahost evolutionary dynamics including the role of immune escape as well as an extensive phylogenomics study to determine to what extent the viral genotype determines virulence and to elucidate its molecular determinants We demonstrate its applicability in LASV research and its potential for broader viral pathogen analysis.