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