ViromeQC

ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichment score for each virome. The score is calculated with respect to the expected prokaryotic markers abundances in reference metagenomes

How it works


ViromeQC calulates the abundance of three microbial markers:

  1. Small Subunit rRNA gene (SSU-rRNA);
  2. Large Subunit rRNA gene (LSU-rRNA);
  3. 31 prokaryotic single-copy markes (AMPHORA2)
and provides an enrichment score (e.g. 5x, meaning the virome is 5 times enriched with respect to an un-enriched metagenome).

The enrichment score is calulated on the pre-computed markers abundances observed in ~2000 metagenomes. However, custom values can also be provided instead.

Software repository, tutorial and supporting material


For detailed tutorial and support, refer to the software repository of viromeQC at: https://bitbucket.org/CibioCM/viromeQC

Citation


If you find this tool useful in your research, please cite our paper:

Moreno Zolfo1 Federica Pinto1 Francesco Asnicar1 Adrian Tett1 Frederic Bushman2 Nicola Segata1

Detecting contamination in viromes using ViromeQC

Nature Biotechnology 2019 10.1038/s41587-019-0334-5

1 Dep. of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy

2 Dep. of Microbiology, University of Pennsylvania - Perelman School of Medicine, Philadelphia (PA) USA