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RSVSim specifications

Information


Unique identifier OMICS_03822
Name RSVSim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.20.0
Stability Stable
Requirements
methods, IRanges, GenomicRanges, ShortRead, Biostrings, rtracklayer, BSgenome.Hsapiens.UCSC.hg19, MASS, R(>=3.0.0), BSgenome.Hsapiens.UCSC.hg19.masked
Maintained Yes

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Publication for RSVSim

RSVSim in publications

 (5)
PMCID: 5436433
PMID: 28521789
DOI: 10.1186/s13059-017-1213-3

[…] regions indicate blocks that do not match the reference., in each experiment we merged two inputs, namely (1) chromosomes 4 and 15 of the yeast genome and (2) a flawed version of (1) produced by rsvsim containing one structural variation, i.e., either a deletion, an inversion (reversal), or a translocation. rsvsim does not allow de novo insertions. for asymmetric tools, the flawed assemblies […]

PMCID: 5850821
PMID: 28486636
DOI: 10.1093/molbev/msx155

[…] where transposons were simulated in the reference genome but not simulated in the bam file. one hundred tes were inserted into regions of the reference genome without pre-existing transposons using rsvsim (), and the performance of temp was evaluated after eight rounds of simulations. te-locate was also run on this set of simulations to evaluate its ability to correctly identify the maintenance […]

PMCID: 5267451
PMID: 28122487
DOI: 10.1186/s12711-017-0286-5

[…] from the umd3.1 bovine genome reference assembly. rearranged chromosomes with 300 randomly inserted sv (100 sv each for deletions, inversions and duplications) were generated with the r package rsvsim []. simulation of short reads was achieved by using wgsim []., we considered several factors that may influence the performance of sv detection: homozygous or heterozygous sv; the sequence […]

PMCID: 5167521
PMID: 27911260
DOI: 10.7554/eLife.20777.056

[…] the sensitivity and specificity of tepid, 100 te insertions (50 copy-paste transpositions, 50 cut-paste transpositions) and 100 te absence variants were simulated in the arabidopsis genome using the rsvsim r package, version 1.7.2 (), and synthetic reads generated from the modified genome at various levels of sequencing coverage using wgsim () (https://github.com/lh3/wgsim). these reads […]

PMCID: 4787836
PMID: 26283183
DOI: 10.1093/nar/gkv831

[…] lasv with several other methods, we generated simulated datasets each with 100 deletions, inversions and tandem duplications randomly inserted across human chromosome 9 using the sv simulation tool rsvsim (). paired-end illumina sequencing reads at 30× coverage with the mean and variance of the fragment size 400 and 50 bp respectively were then simulated using the pirs software (). the process […]


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RSVSim institution(s)
Institute of Medical Informatics, University of Münster, Münster, Germany

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