nf-core/vipr
Assembly and intrahost / low-frequency variant calling for viral samples
This pipeline is archived and no longer maintained.
Archived pipelines can still be used, but may be outdated and will not receive bugfixes.
22.10.6.
Learn more.
Introduction
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:
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:
Plenty of people provided essential feedback, including:
- October SESSIONS
- Paola Florez DE SESSIONS
- ZHU Yuan
- Shuzhen SIM
- CHU Wenhan Collins