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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

[…] img/m [] and mg-rast [] platforms as well as the ebi metagenomics portal [] continue to offer their services, serving as valuable resources to the community. a different approach is followed by clovr [], which is provided as a virtual machine image, and to a certain degree by cyverse [], a web-based infrastructure for data analysis that also provides a limited range of applications […]


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

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

[…] 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 […]


Identification of fungi in shotgun metagenomics datasets

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

[…] 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 […]


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

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

[…] 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., fifty-milliliter cultures of gbs were grown in tsb or new granada […]


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

PMCID: 5620648
PMID: 28895889
DOI: 10.3390/microorganisms5030057

[…] 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:, total rna from p. acnes (kpa171202 (type ib), and 12.1.l1 (type ia)) grown under anaerobic conditions to the exponential and stationary […]


Scalability and Validation of Big Data Bioinformatics Software

PMCID: 5537105
PMID: 28794828
DOI: 10.1016/j.csbj.2017.07.002

[…] ‘instance’. in bioinformatics, iaas solutions are typically virtual machine (vm) containers in which a user can deploy to their own customised instance on the cloud. both cloudbiolinux and clovr are examples of iaas solutions for performing bioinformatics analysis. some cloud providers, especially those targeted for researchers, also provide some pre-built vm snapshots or images […]

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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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