Published November 20, 2019
| Version 1.0
Software
Open
ViromeQC
- 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
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
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