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

Views: 247   Downloads: 5

Created: 14th May 2020 at 15:52

Last updated: 2nd Jun 2020 at 11:50

Last used: 25th Nov 2020 at 14:50

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