CloVR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CloVR

Tool usage distribution map

This map represents all the scientific publications referring to CloVR per scientific context
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Associated diseases

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Popular tool citations

chevron_left Genome assembly Functional annotation Bioinformatics workflows Prediction-Based Taxonomic Homology-Based Taxonomic Nucleotide sequence homology search Functional profile prediction chevron_right
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CloVR specifications


Unique identifier OMICS_01216
Name CloVR
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Parallelization MapReduce
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.0-RC9
Stability Stable
VMWare, VirtualBox virtual machine players
High performance computing Yes
Maintained Yes


No version available


  • person_outline Samuel Angiuoli
  • person_outline Florian Fricke

Publication for CloVR

CloVR citations


Flexible metagenome analysis using the MGX framework

PMCID: 5937802
PMID: 29690922
DOI: 10.1186/s40168-018-0460-1

[…] is, most notably MG-RAST, IMG/M, and the EBI metagenomics portal. Also, web-based infrastructures such as CyVerse provide some basic capabilities to process metagenome data, and virtual machines like CloVR enable metagenome processing on local or cloud-based resources (Table ). MG-RAST, IMG/M, and the EBI metagenomics website all provide a predefined analysis pipeline offering quality control and […]


Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities

PLoS One
PMCID: 5839586
PMID: 29509797
DOI: 10.1371/journal.pone.0193820

[…] yML with the generalized time-reversible substitution model, the gamma-distributed rate heterogeneity, and midpoint rooting [, ].Genome assemblies of the 19 ST5 isolates were further annotated in the CloVR-Microbe pipeline []. Identified SaPIs and plasmids were compared to SaPI and S. aureus plasmid sequences in the GenBank database using Mauve []. In addition, the 19 annotated ST5 genome assembli […]


Identification of fungi in shotgun metagenomics datasets

PLoS One
PMCID: 5812651
PMID: 29444186
DOI: 10.1371/journal.pone.0192898

[…] arcode sequence for fungi []. Several pipelines have been developed to identify specific fungal species and calculate the frequency of each species from ITS data, including Plutof, Clotu, PIPITS, and CloVR-ITS [–]. BioMaS, Mothur and Qiime can be used with both bacterial and fungal amplicon reads [–].The second approach identifies species from shotgun metagenomes. Most tools use custom-built datab […]


Bacterial Microbiota of Rice Roots: 16S Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community

PMCID: 5874628
PMID: 29439478
DOI: 10.3390/microorganisms6010014
call_split See protocol

[…] Reads were initially mapped against O. sativa mitochondrial (NC_011033) and plastidial genomes (NC_001320). Unmapped reads were further processed. We used CloVR 1.0 RC9 [] on the Amazon Elastic Compute Cloud (EC2) to run the QIIME workflow “” []. Within the QIIME workflow: (i) We set the minimum and maximum sequence length […]


The Streptococcus agalactiae Stringent Response Enhances Virulence and Persistence in Human Blood

Infect Immun
PMCID: 5736797
PMID: 29109175
DOI: 10.1128/IAI.00612-17

[…] criptome comparisons, RNA-seq results from the two strains grown under SR and non-SR conditions were normalized for read numbers. Orthologous genes shared by the two strains were identified using the CloVR-Comparative pipeline (, ) and Sybil (). Normalized read counts for orthologs were compared directly using in-house scripts. […]


The Skin Bacterium Propionibacterium acnes Employs Two Variants of Hyaluronate Lyase with Distinct Properties

PMCID: 5620648
PMID: 28895889
DOI: 10.3390/microorganisms5030057
call_split See protocol

[…] ithms, respectively. To compare the genomic context of the hyl gene, we used Sybil []. The Sybil database for P. acnes was established and described previously [] and is accessible here: […]

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CloVR institution(s)
Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
CloVR funding source(s)
Supported by funds from the National Human Genome Research Institute, NIH/NHGRI, ARRA under Grant No. RC2 HG005597-01, the National Science Foundation, NSF, under Grant No. 0949201 and the Amazon Web Services in Education Research Grants program.

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