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RADtools specifications

Information


Unique identifier OMICS_03727
Name RADtools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.2.4
Stability Stable
Requirements
R::Parallel::ForkManager
Maintained Yes

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  • person_outline John Davey <>

Publication for RADtools

RADtools in publications

 (13)
PMCID: 5773296
PMID: 29375779
DOI: 10.1002/ece3.3706

[…] of the freshwater snail biomphalaria glabrata (ncbi accession number: apka00000000.1.). the in silico estimation was conducted using the script genomecut.pl (rozenberg, https://github.com/evoeco/radtools/) and resulted in an average cut frequency of 306 bp for csp6i and of 9785 bp for psti. in most cases, the pcr was successful when using 2 μl of dna. if the dna concentration of a sample […]

PMCID: 5592941
PMID: 28751500
DOI: 10.1534/g3.117.300082

[…] of tens of thousands of snp markers in model and nonmodel organisms. while several snp genotyping tools have been developed for snp discovery, including gatk (), stacks (, ), samtools () and radtools (), stacks is recommended for ddrad-seq projects, as it uses a multinomial-based likelihood model to call snps, which incorporates a bounded snp model., in this study, we employed […]

PMCID: 4991039
PMID: 27538483
DOI: 10.1186/s12864-016-3003-9

[…] can be performed with tools such as samtools [] and gatk []. for species without available reference genomes, de novo methods have to be employed to generate rad markers, which include stacks [], radtools [], rapid [], rainbow [] and pyrad []. although many tools are available for rad-seq data analyses, there is still much room to improve the analytical strategies for obtaining more accurate […]

PMCID: 4748748
PMID: 26430059
DOI: 10.1093/sysbio/syv076

[…] reads. , the libraries were demultiplexed into individual samples according to the respective barcode combinations by allowing for single errors at the barcodes using the radpools module of the radtools v. 1.2.4 package ( ). the 84 individual files have been further imported in the clc genomic workbench v. 6.5 (qiagen) and trimmed/filtered to retain only full-length (i.e., 94 bp […]

PMCID: 4815504
PMID: 25757406
DOI: 10.1038/hdy.2015.10

[…] used to process and analyse rad-seq data is summarised in . sequencing quality of each rad library was assessed with fastqc (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc). we then used radtools () to trim reads to 70 bp and remove sequences lacking a correct barcode or sbfi restriction site, or with quality score <20 at any position. to account for sequencing errors, a fuzzy […]

RADtools institution(s)
Department of Zoology, University of Cambridge, Cambridge, UK; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK; Department of Entomology, Texas A&M University, College Station, TX, USA; Department of Entomology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, USA; Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany; The GenePool Genomics Facility, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
RADtools funding source(s)
This work was supported by the Biotechnology and Biological Sciences Research Council [grants No. G00661X, No. F021135, No. RG47616]; the Medical Research Council [grant No. G0900740], the Max-Planck-Gesellschaft and the Natural Environment Research Council [grant No. R8/H10/56].

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