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:

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

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:

• Sessions et. al., PLoS Negl Trop Dis., 2015
• Sim et al., PLoS Negl Trop Dis., 2015

Plenty of people provided essential feedback, including:

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