nf-core/vipr
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nf-core/vipr


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install with bioconda Docker Container available https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg
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:

Plenty of people provided essential feedback, including:

help Creators and Submitter
Creator
  • Andreas Wilm and October SESSIONS and Paola Florez DE SESSIONS and ZHU Yuan and Shuzhen SIM and CHU Wenhan Collins
Submitter
License
Activity

Views: 270   Downloads: 10

Created: 14th May 2020 at 15:42

Last updated: 2nd Jun 2020 at 11:49

Last used: 11th Aug 2020 at 06:42

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