nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Pipeline Steps

StepMain program/s
Trimming, combining of read-pairs per sample and QCSkewer, FastQC
Metagenomics classification / Sample purityKraken
Assembly to contigsBBtools’ Tadpole
Assembly polishingViPR Tools
Mapping to assemblyBWA, LoFreq
Low frequency variant callingLoFreq
Coverage and variant AF plots (two processes)Bedtools, ViPR Tools


Documentation about the pipeline can be found in the docs/ directory:

  1. Installation and configuration
  2. Running the pipeline
  3. Output and how to interpret the results


This pipeline was originally developed by Andreas Wilm (andreas-wilm) at Genome Institute of Singapore. It started out as an ecosystem around LoFreq and went through a couple of iterations. The current version had three predecessors ViPR 1, ViPR 2 and ViPR 3

An incomplete list of publications using (previous versions of) ViPR:

Plenty of people provided essential feedback, including: