nf-core/vipr

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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:

1. Installation and configuration
2. Running the pipeline
3. Output and how to interpret the results

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:

• Sessions et. al., PLoS Negl Trop Dis., 2015
• Sim et al., PLoS Negl Trop Dis., 2015

Plenty of people provided essential feedback, including:

• October SESSIONS
• Paola Florez DE SESSIONS
• ZHU Yuan
• Shuzhen SIM
• CHU Wenhan Collins