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RADtyping specifications


Unique identifier OMICS_03726
Name RADtyping
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained No


No version available


This tool is not available anymore.

Publication for RADtyping

RADtyping citations


Characterization of Population Genetic Structure of red swamp crayfish, Procambarus clarkii, in China

Sci Rep
PMCID: 5883011
PMID: 29615795
DOI: 10.1038/s41598-018-23986-z

[…] nd −r 0 allowing four mismatches. The sequences that aligned with only one location were regarded as unique tags and the expected potential markers. The aligned reads were performed SNP calling using RADtyping with default Posterior probability is calculated for two possible genotypes (homozygote and heterozygote) at a given locus using a maximum likelihood approach. To look for the relationship b […]


A high resolution genetic linkage map and QTL fine mapping for growth related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus)

BMC Genomics
PMCID: 5879560
PMID: 29609551
DOI: 10.1186/s12864-018-4613-1

[…] ons with quality of less than 20) or mitochondrial origins were removed. The remaining trimmed reads with 32 bp in length were used for subsequent analysis. De novo genotyping was performed using the RADtyping program v1.0 []. Using this software, both codominant and dominant markers were identified and genotyped. […]


Unveiling the Identity of Wenwan Walnuts and Phylogenetic Relationships of Asian Juglans Species Using Restriction Site Associated DNA Sequencing

Front Plant Sci
PMCID: 5641410
PMID: 29067029
DOI: 10.3389/fpls.2017.01708

[…] each read, and those mapped onto more than one position in the genomic reference sequence were excluded (–r 0). The match mode was set to “find the best hits” (–M 4). The SNPs were filtered with the RADtyping program () using the following criteria: (1) Polymorphic loci with more than two alleles were deleted; (2) Segregating markers that could be genotyped in at least 80% of the individuals were […]


Whole Genome Restriction Mapping by “Subhaploid” Based RAD Sequencing: An Efficient and Flexible Approach for Physical Mapping and Genome Scaffolding

PMCID: 5500127
PMID: 28468906
DOI: 10.1534/genetics.117.200303

[…] Seq2000 sequencer.Raw reads were first preprocessed to remove unreliable ones with no restriction site, ambiguous basecalls (N), long homopolymer regions, or excessive low-quality positions using the RADtyping program under default parameters (). The obtained high-quality reads were further filtered by mapping against ∼10× MiSeq PE300 WGS data set (generated in this study) using the SOAP2 program […]


Evaluation of the 2b RAD method for genomic selection in scallop breeding

Sci Rep
PMCID: 4709697
PMID: 26754638
DOI: 10.1038/srep19244

[…] b-RAD libraries were prepared following the protocol developed by Wang et al. and were subject to single-end sequencing using an Illumina HiSeq2000 platform. 2b-RAD genotyping was performed using the RADtyping program v1.5 with default parameters. Segregating markers that could be genotyped in at least 70% of the individuals with minor allele frequency (>5%) were retained for subsequent analysis. […]


Construction of a High Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus

Sci Rep
PMCID: 4594301
PMID: 26439740
DOI: 10.1038/srep14852

[…] forward for analysis ( and Additional File A1). The raw read data were archived at the NCBI Sequence Read Archive (SRA) under Accession Number PRJNA274721.The genotyping procedure was performed using RADtyping v1.0. The result showed that clustering of parental reads generated 186,692 representative reference tags, including 125,616 codominant tags and 61,076 dominant tags, 7769 low quality tags w […]


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RADtyping institution(s)
Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong Province, China

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