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viRome specifications

Information


Unique identifier OMICS_19248
Name viRome
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some aligned data.
Input format BAM
Output data A variety of graphs and reports.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.7
Stability Stable
Maintained No

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Publication for viRome

viRome citations

 (4)
library_books

A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

2017
J Virol
PMCID: 5533899
PMID: 28515299
DOI: 10.1128/JVI.00158-17

[…] ly exclude viruses that require different preparation methods or that are not amenable to crude extraction. Importantly, our use of metagenomic techniques was crucial in revealing a more complete bee virome, as many highly divergent viruses can be detected only at the sequence level (, ). Our study was also aided by the recent explosion in novel virus genomes (, , ), which provides a more comprehe […]

library_books

The Antiviral RNAi Response in Vector and Non vector Cells against Orthobunyaviruses

2017
PLoS Negl Trop Dis
PMCID: 5245901
PMID: 28060823
DOI: 10.1371/journal.pntd.0005272

[…] MOI of 10. At 24 hours p.i., RNA was isolated from individual wells using 1 ml TRIzol (Life Technologies) followed by purification, sequencing, analysis and mapping of virus specific small RNAs using viRome []. Small RNA sequences were submitted to the European Nucleotide Archive (accession number PRJEB15203). Data for SBV are referenced under []. The actual number of reads for each experiment is […]

library_books

piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis

2015
PLoS Genet
PMCID: 4524669
PMID: 26241928
DOI: 10.1371/journal.pgen.1005332

[…] s. Reads were normalized by non-unique mappers to the D. virilis reference genome using BWA.aln defaults. Calculations for ping-pong percent [] and density of piRNA pairs were done with the R package viRome (http://www.ark-genomics.org/bioinformatics/virome), with some modifications. For genic small RNA analysis, reads were mapped uniquely with BWA.aln to the D. virilis reference genome, using def […]

library_books

Transcriptome Analysis of Bombyx mori Larval Midgut during Persistent and Pathogenic Cytoplasmic Polyhedrosis Virus Infection

2015
PLoS One
PMCID: 4376736
PMID: 25816294
DOI: 10.1371/journal.pone.0121447

[…] Bombyx miRNA miRBASE 19 database were subsequently mapped against the BmCPV genome to find vsRNAs originating from the virus. Small RNA length distribution graphs were produced in R [] by use of the viRome package (http://www.ark-genomics.org/bioinformatics/virome). The sequences from the mRNA and small RNA libraries of all 4 samples were submitted to the European Nucleotide Archive (Accession Nu […]

Citations

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viRome institution(s)
ARK-Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
viRome funding source(s)
Supported by UK Biotechnology and Biological Sciences Research Council (BBSRC) (BB/J004243/1; BB/J004235/1), UK Medical Research Council (MRC) and The Netherlands Organisation for Scientific Research NWO (Rubicon Fellowship number: 825.10.021).

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