ViromeScan statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

ViromeScan specifications


Unique identifier OMICS_11254
Name ViromeScan
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Input files should be single-end or paired-end reads in fastq format (for paired-end reads compressed files in gzip, bzip2 and zip formats are also accepted) retrieved from shotgun sequencing or RNA-seq.
Operating system Unix/Linux, Mac OS
Programming languages Java, Perl, R, Shell (Bash)
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Bowtie2, Bmtagger, Picard tools
Maintained Yes


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  • person_outline Simone Rampelli <>

Publication for ViromeScan

ViromeScan in publications

PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] human reference genome is often used, as is the case with srsa (isakov et al., ), rins (bhaduri et al., ), virushunter (zhao et al., ), mepic (takeuchi et al., ), ensemble assembler (deng et al., ), viromescan (rampelli et al., ), and metashot (fosso et al., ). depending on the sample type and expected contaminants, this can be extended to filtering rrna, mtrna, mrna, bacterial or fungal […]

PMCID: 5855605
PMID: 29382070
DOI: 10.3390/ijms19020383

[…] are required to carry out the assembly []., in addition, many of the bioinformatic tools currently available for shotgun metagenomics do not allow efficient viruses estimation. in this context, viromescan is an open-source tool, specifically developed to analyze virome taxonomy and relative abundance directly from shotgun metagenomic data []. viromescan is able to enrich viral reads […]

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ViromeScan institution(s)
Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy

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