nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples.
The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
| Step | Main program/s |
|---|---|
| Trimming, combining of read-pairs per sample and QC | Skewer, FastQC |
| Decontamination | decont |
| Metagenomics classifcation / 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 at the Genome Institute of Singapore by Andreas Wilm. It started out as an ecosystem around LoFreq an 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
nfcore/vipr is used mainly by the Bioinformatics Core of the Genome Institue of Singapore. If you use this pipeline too, please let us know in an issue and we will add you to the list.
 |
Genome Institute of Singapore | https://www.a-star.edu.sg/gis/ |
 |
iGap | http://www.igap.io |