Version 1

Workflow Type: Nextflow


Build Status Nextflow Gitter

install with bioconda Docker Container available

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:

Version History

Version 1 (earliest) Created 14th May 2020 at 15:42 by Laura Rodriguez-Navas

Added/updated 1 files

Open master adac140
help Creators and Submitter
Not specified
Additional credit

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


Views: 4137   Downloads: 525

Created: 14th May 2020 at 15:42

Last updated: 2nd Jun 2020 at 11:49

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