CloVR protocols

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CloVR specifications

Information


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
Requirements
VMWare, VirtualBox virtual machine players
High performance computing Yes
Maintained Yes

Versioning


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Maintainers


  • person_outline Samuel Angiuoli <>
  • person_outline Florian Fricke <>

Publication for CloVR

CloVR in pipelines

 (6)
2017
PMCID: 5339403
PMID: 28161492
DOI: 10.1016/j.gpb.2016.11.001

[…] the unigene did not show any similarity with other unigenes., unigene sequences were first aligned by blastx (https://blast.ncbi.nlm.nih.gov/blast.cgi) to protein databases including cog (http://clovr.org/docs/clusters-of-orthologous-groups-cogs/), swiss-prot (https://www.ebi.ac.uk/uniprot), and kegg (http://www.genome.jp/kegg) using a cut-off e-value of 1e–5 , . these sequences […]

2017
PMCID: 5372535
PMID: 28264491
DOI: 10.3390/ijms18030519

[…] 5,000 bp region downstream of waac were reannotated in each genome. gene prediction was performed with glimmer v.3.0.2 [] and hand-curated. comparison of the genetic regions was performed using the clovr comparative pipeline [] and explored using sybil []., the predicted protein sequence of one arbitrarily selected o-antigen ligase from each wa region 1 genomic organization was retrieved […]

2017
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: http://sybil-clovr.igs.umaryland.edu/sybil/christianscholz_pacnes_sybil., total rna from p. acnes (kpa171202 (type ib), and 12.1.l1 (type ia)) grown under anaerobic conditions to the exponential and stationary […]

2015
PMCID: 4640099
PMID: 26515720
DOI: 10.1038/ncomms9754

[…] genomes under manual correction. a total of 186 strains of typhimurium with sra data produced by illumina paired-end technology were submitted for de novo genome assembly and annotation by using clovr. clovr used both virtual machine and cloud computation technology for high-throughput data processing. all the annotated genomic data were uploaded into seed for further data storage, sequence […]

2014
PMCID: 4137656
PMID: 25165636
DOI: 10.7717/peerj.529

[…] gene or concatenated whole genome cds alignments with any alignments shorter than 30 amino acids removed (), using the program dnasp (). genomic synteny was assessed with the cloud virtual resource (clovr) comparative pipeline () and sybil synteny gradient viewer () using the data intensive academic grid (diag) at the university of maryland. the number of phage and phage-associated genes […]


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CloVR in publications

 (51)
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 […]

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 […]

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 […]

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 […]

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: http://sybil-clovr.igs.umaryland.edu/sybil/christianscholz_pacnes_sybil., total rna from p. acnes (kpa171202 (type ib), and 12.1.l1 (type ia)) grown under anaerobic conditions to the exponential and stationary […]


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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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