This repository contains the code of Viralflow, a workflow to performs a reference guided genome assembly of non-segmented viruses written in Nextflow. The workflow was developed to work with Illumina paired-end reads. Tests with other technologies should be performed.
If you use this workflow for academic purposes, please cite: ViralFlow v1.0—a computational workflow for streamlining viral genomic surveillance.
The official documentation could be accessed here in English or here in Portuguese.
ViralFlow is a nextflow pipeline and should be treated as such, check vfnext/ for more detail. A wrapper for the pipeline is provided for user convenience.