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 |
| Contig library dereplication | Vclust, at the MIUViG species thresholds |
| Abundance estimation | CoverM |
| Binning | vRhyme |
| Viral contig identification | geNomad, CheckV and VIBRANT; VirSorter2 then prepares the affi-contigs table DRAM-v needs |
| Auxiliary gene (AMG/AReG/APG) calling | CheckAMG |
| Gene function annotation | DRAM-v, EggNOG and abricate |
| Viral replication cycle prediction | BACPHLIP or Replidec |
| Viral taxonomy annotation | VITAP and vConTACT3 |
| Viral-host prediction | iPHoP |
| Results object and visualization | vpfkit assembles a TreeSummarizedExperiment and provides the Shiny viewer and the Quarto report; MultiQC summarises the run |
The pipeline's headline output is that TreeSummarizedExperiment: one object carrying the
abundance assays, every per-contig annotation and the sample metadata, ready for analysis in
R. Pass --sample_metadata or its colData will hold nothing but the sample names.
Requires Nextflow 26.04 or newer — see Installation.
Tutorial
A tutorial is available so you can quickly get the gist of the pipeline's capabilities.