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nfcore/vipr

By nfcore

•Updated almost 8 years ago

A docker container for VIPR

Image
Machine learning & AI
Data science
0

1.6K

nfcore/vipr repository overview

nf-core/vipr

Build Status Nextflow Gitter

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

⁠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
StepMain program/s
Trimming, combining of read-pairs per sample and QCSkewer, FastQC
Decontaminationdecont
Metagenomics classification / Sample purityKraken
Assembly to contigsBBtools' Tadpole
Assembly polishingViPR Tools
Mapping to assemblyBWA, LoFreq
Low frequency variant callingLoFreq
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:

Tag summary

Content type

Image

Digest

Size

626.4 MB

Last updated

almost 8 years ago

docker pull nfcore/vipr