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.
|Trimming, combining of read-pairs per sample and QC||Skewer, FastQC|
|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
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: