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

Step Main program/s
Trimming, combining of read-pairs per sample and QC Skewer, FastQC
Decontamination decont
Metagenomics classification / Sample purity Kraken
Assembly to contigs BBtools' Tadpole
Assembly polishing ViPR Tools
Mapping to assembly BWA, LoFreq
Low frequency variant calling LoFreq
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: