Welcome to ViroProfiler pipeline documentation
About
ViroProfiler is a pipeline designed to provide an easy-to-use framework for performing a comprehensive analyses of viral metagenomics data. It is developed with Nextflow and Docker. It can detect and characterize viral sequences and communities recovered from metagenomics data.
Workflow
The pipeline's main steps are:
| Pipeline modules | Used software or databases |
|---|---|
| Genome assembly | metaSPAdes |
| Binning | vRhyme or phamb |
| Viral contig identification | VirSorter2, DeepVirFinder, VIBRANT and CheckV |
| Gene function annotation | DRAM-v, EggNOG and abricate |
| Viral replication cycle prediction | BACPHLIP or Replidec |
| Viral taxonomy annotation | vConTACT2 and MMseqs2 taxonomy |
| Viral-host prediction | iPhoP |
| Results visualization | MulqiQC, R Markdown and Shiny |
Tutorial
A tutorial is available so you can quickly get the gist of the pipeline's capabilities.