Published November 20, 2019 | Version 1.0
Software Open

ViromeQC

Creators

  • 1. CIBIO, University of Trento

Description

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. ViromeQC can be applied to FASTQ raw sequencing files from VLP enriched shotgun sequencing.

Cite:

Zolfo, M., Pinto, F., Asnicar, F. et al.
Detecting contamination in viromes using ViromeQC. Nat Biotechnology (2019)
https://doi.org/10.1038/s41587-019-0334-5

Download ViromeQC at: https://github.com/SegataLab/viromeqc

This upload contains:

  • The SSU and LSU rRNA gene sequences from SILVA (release 132)
  • The sequences of 31 Single-Copy bacterial markers from AMPHORA2 

Files

amphora_markers.zip

Files (1.2 GB)

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Additional details

Related works

Is derived from
Journal article: 10.1038/s41587-019-0334-5 (DOI)
Is part of
Software documentation: https://github.com/SegataLab/viromeqc (URL)

Funding

MetaPG – Culture-free strain-level population genomics to identify disappearing human-associated microbes in the westernized world 716575
European Commission

References

  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tool, Nucleic Acids Research
  • Martin Wu, Alexandra J. Scott, Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2, Bioinformatics