Nextflow Registry | nf-core/vipr

nf-core/vipr

Assembly and intrahost / low-frequency variant calling for viral samples

genome-assembly metagenomics variant-calling viral viral-genomics viral-metagenomics viral-ngs virus viruses

Version: 0.0.0-6eef3b3 Git revision: 6eef3b32eac4ac3979c7a45e61188e8a3628aa68 Commit: Content hash:

Run:

Repository: nf-core/vipr

Workflow: main.nf

Website: https://nf-co.re/vipr

Build Status

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Introduction

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

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

Credits

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:

October SESSIONS
Paola Florez DE SESSIONS
ZHU Yuan
Shuzhen SIM
CHU Wenhan Collins

Version	Git revision	Released	Status
0.0.0-6eef3b3	`6eef3b32eac4ac3979c7a45e61188e8a3628aa68`	12 Oct 2026 16:55:26 (UTC)