From Whole Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool

Simone Rampelli; Silvia Turroni; Marco Candela

doi:10.1007/978-1-0716-3515-5_2

From Whole Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool

Methods Mol Biol. 2024:2732:23-28. doi: 10.1007/978-1-0716-3515-5_2.

Authors

Simone Rampelli¹, Silvia Turroni², Marco Candela²

Affiliations

¹ Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy. simone.rampelli@unibo.it.
² Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.

PMID: 38060115
DOI: 10.1007/978-1-0716-3515-5_2

Abstract

ViromeScan is an innovative metagenomic analysis tool that allows characterizing the taxonomy of viral communities from raw data of metagenomics sequencing, efficiently denoising samples from reads of other microorganisms. This means that users can use the same shotgun metagenomic sequencing data to fully characterize complex microbial ecosystems, including bacteria and viruses. Here we describe the analysis procedure with some examples, illustrating the processes computed by ViromeScan from raw data to the final output.

Keywords: Bioinformatics; Pipeline; Sequencing; Shotgun metagenomics; Virome.

MeSH terms

Ecosystem
Genome, Viral
High-Throughput Nucleotide Sequencing / methods
Metagenome
Metagenomics / methods
Software*
Viruses* / genetics
Whole Genome Sequencing / methods