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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline John Davey

Publication for RADtools

RADtools citations

 (16)
library_books

Genome‐wide single‐nucleotide polymorphism data reveal cryptic species within cryptic freshwater snail species—The case of the Ancylus fluviatilis species complex

2017
Ecol Evol
PMCID: 5773296
PMID: 29375779
DOI: 10.1002/ece3.3706

[…] nome 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 afte […]

library_books

Genome wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae)

2017
Sci Rep
PMCID: 5599554
PMID: 28912480
DOI: 10.1038/s41598-017-11367-x

[…] RAD sequencing reads are used de novo, generating large marker sets where no reference genome is available. Several tools have been developed to produce RAD marker sets de novo, including Stacks and RADtools. Pan et al. tested and compared SNP calling using the UNEAK, Stacks and bowtie2-GATK pipelines for genotyping-by-sequencing (GBS) data in nine individuals of the three pine species, and found […]

library_books

RAD sequencing resolves fine scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity

2017
R Soc Open Sci
PMCID: 5367306
PMID: 28386419
DOI: 10.1098/rsos.160548

[…] and demultiplexing of raw reads were performed using the program trimmomatric [] and the scripts ‘double_indexing.pl’ and ‘preprocess_radtags.pl’ [], which are available at https://github.com/evoeco/radtools. Then, processing of the cleaned data was carried out using Stacks v. 1.35 []: denovo_map.pl was used to assemble tags and rxstacks was then utilized to increase the quality of the called gen […]

library_books

De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole genome sequencing technologies

2016
BMC Genomics
PMCID: 4991039
PMID: 27538483
DOI: 10.1186/s12864-016-3003-9

[…] ing 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 a […]

library_books

TagDigger: user friendly extraction of read counts from GBS and RAD seq data

2016
Source Code Biol Med
PMCID: 4940913
PMID: 27408618
DOI: 10.1186/s13029-016-0057-7

[…] l to extract those values for analysis. Stacks [] exports read counts, although it has the disadvantage of only running on Unix-like operating systems. pyRAD [] exports genotypes but not read counts. RADtools [] exports read counts in a custom format, but is no longer being updated since Stacks was determined to have superior genotyping and performance []. RADtools also does not allow barcode leng […]

library_books

Processes Driving the Adaptive Radiation of a Tropical Tree ( Diospyros , Ebenaceae) in New Caledonia, a Biodiversity Hotspot

2015
Syst Biol
PMCID: 4748748
PMID: 26430059
DOI: 10.1093/sysbio/syv076

[…] 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 after barco […]


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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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