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Protocols

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


No version available

Maintainers


  • person_outline Samuel Angiuoli
  • person_outline Florian Fricke

Publication for CloVR

CloVR citations

 (70)
library_books

Flexible metagenome analysis using the MGX framework

2018
Microbiome
PMCID: 5937802
PMID: 29690922
DOI: 10.1186/s40168-018-0460-1

[…] abases. While IMG/M only accepts submissions of pre-assembled data for metagenomes sequenced outside of the JGI [], MG-RAST and the EBI metagenomics portal are available without such restrictions.The CloVR-Metagenomics protocol only provides very limited functionality in the form of a simple BLAST-based pipeline used for taxonomic and functional assignment with no preceding quality control; in add […]

library_books

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

2018
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 […]

library_books

Identification of fungi in shotgun metagenomics datasets

2018
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 […]

call_split

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

2018
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 “pick_otus_through_otu_tables.py” []. Within the QIIME workflow: (i) We set the minimum and maximum sequence length […]

library_books

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

2017
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. […]

call_split

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

2017
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: http://sybil-clovr.igs.umaryland.edu/sybil/ChristianScholz_Pacnes_sybil. […]

Citations

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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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