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
Metagenomics classification / Sample purity
Assembly to contigs
Mapping to assembly
Low frequency variant calling
Coverage and variant AF plots (two processes)
Bedtools, ViPR Tools
Documentation about the pipeline can be found in the
It started out as an ecosystem around LoFreq and went through a couple of iterations.
An incomplete list of publications using (previous versions of) ViPR:
Plenty of people provided essential feedback, including: