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.
| 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:
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