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Protocols

SimRAD specifications

Information


Unique identifier OMICS_09148
Name SimRAD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.96
Stability Stable
Requirements
stats, graphics, ShortRead, Biostrings, zlibbioc, seqinr
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Olivier Lepais

Publication for SimRAD

SimRAD citations

 (8)
library_books

Reference based RADseq resolves robust relationships among closely related species of lichen forming fungi using metagenomic DNA

2017
Sci Rep
PMCID: 5575168
PMID: 28852019
DOI: 10.1038/s41598-017-09906-7

[…] lation.RADseq datasets of the de novo reference genome of R. melanophthalma sensu stricto and the 30 consensus sequences of the R. melanophthalma species complex were simulated by using the R package SimRAD. After an initial test using different cut sites on the reference sequence to select for the best restriction enzyme, we in silico digested all 30 genome sequences with ApeKI (5-cutter with one […]

library_books

SNP discovery and genotyping using Genotyping by Sequencing in Pekin ducks

2016
Sci Rep
PMCID: 5109183
PMID: 27845353
DOI: 10.1038/srep36223

[…] sing the standard phenol/chloroform method. An in silico digestion of the duck reference genome (BGI 1.0, Ensemble 82) was performed to choose the appropriate restriction endonuclease using R package SimRAD. According to the results of simulated digestion, 100 ug genomic DNA was digested with restriction endonuclease MseI, which recognizes a 4-bp sequence (TTAA) and creates a 2-bp overhang (). The […]

library_books

Quantifying the Escape Mortality of Trawl Caught Antarctic Krill (Euphausia superba)

2016
PLoS One
PMCID: 5021277
PMID: 27622510
DOI: 10.1371/journal.pone.0162311

[…] during February 2015. The vessel used was the FV Juvel (Olympic AS) a Norwegian, 99.5 m, 6000 kw/8158 hp (main engine) commercial ramp trawler. Trawls were performed on acoustic registrations, using Simrad EK60 General Purpose Transceivers connected to hull mounted ES60 transducers. The trawl used for the experiment had a 6 × 6 m mouth opening, fitted with a 7 mm cover for the 16 mm codend. The t […]

library_books

Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

2016
Ecol Evol
PMCID: 4851556
PMID: 27195104
DOI: 10.1002/ece3.2110

[…] Number of RADtag was predicted using the R package SimRAD (Lepais and Weir ) using the haploid nuclear DNA content (C‐value) published for M. galloprovincialis of 1.92 pg (Rodríguez‐Juíz et al. ) equivalent to an haploid genome size of 1877.76 Mb. We […]

library_books

Predicting RAD seq Marker Numbers across the Eukaryotic Tree of Life

2015
Genome Biol Evol
PMCID: 4700943
PMID: 26537225
DOI: 10.1093/gbe/evv210

[…] For library preparation protocols in which a fragment size selection step is done without a prior shearing step, for example, ddRAD () and ezRAD (), the “size.select” function of the software package SimRAD () constitutes a valuable complementary study design tool. If a new genome assembly becomes available for the target species and/or the researcher wishes to evaluate an additional restriction e […]

library_books

Short Term Fidelity, Habitat Use and Vertical Movement Behavior of the Black Rockfish Sebastes schlegelii as Determined by Acoustic Telemetry

2015
PLoS One
PMCID: 4556453
PMID: 26322604
DOI: 10.1371/journal.pone.0134381

[…] SeaBotix, California, USA) and the dive operated stereo-video system (stereo-DOV) []. Video examples of the bottom types are provided in – Videos. The spatial coverage of seagrass was quantified by a Simrad EY60 split-beam device run at 200 kHz along closely spaced routes parallel to the shelf in the shallow waters of the Qiansan Islets (< 20 m deep, see for visualization of the trajectory), and […]

Citations

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SimRAD institution(s)
INRA, UMR 1224, Ecologie Comportementale et Biologie des Populations de Poissons, INRA, Saint Pée sur Nivelle, France; Univ Pau & Pays Adour, UMR 1224, Ecologie Comportementale et Biologie des Populations de Poissons, UFR Sciences et Techniques de la Côte Basque, Univ Pau and Pays Adour, Anglet, France

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