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RADtyping specifications

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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

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Publication for RADtyping

RADtyping citations

 (10)
library_books

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

2018
PMCID: 5883011
PMID: 29615795
DOI: 10.1038/s41598-018-23986-z

[…] −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 […]

library_books

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)

2018
PMCID: 5879560
PMID: 29609551
DOI: 10.1186/s12864-018-4613-1

[…] 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., a total of 1500 genomic and transcript-associated ssr markers previously published […]

library_books

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

2017
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 […]

library_books

High Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge)

2017
PMCID: 5511184
PMID: 28710433
DOI: 10.1038/s41598-017-05756-5

[…] low-quality (score <10) positions were removed. the remaining trimmed, high-quality reads formed the basis of subsequent analyses. de novo 2b-rad genotyping was performed using the program radtyping v1.0., lm × ll (markers from the pollen parent) or nn × np (markers from the seed parent) were categorized as the dominant markers, which segregated in a 1:1 ratio in the map population. […]

library_books

A High Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp (Carassius auratus) Using 2b RAD Sequencing

2017
PMCID: 5555455
PMID: 28600439
DOI: 10.1534/g3.117.041376

[…] with a quality <20) or mitochondrial origins were removed. the remaining trimmed reads with 32 bp in length were used for subsequent analysis. filtered reads were analyzed with the software radtyping program v1.0 () for de novo 2b-rad genotyping. this software used stringent criteria in filtering candidate markers, and only those loci with at least four reads supporting were kept […]

library_books

Effects of marker density and population structure on the genomic prediction accuracy for growth trait in Pacific white shrimp Litopenaeus vannamei

2017
PMCID: 5436459
PMID: 28514941
DOI: 10.1186/s12863-017-0507-5

[…] briefly, the 2b–rad libraries were prepared following the standard protocol [], and then they were pooled for sequencing using illumina hiseq x ten platform. the genotyping was performed using the radtyping program v1.537 with default parameters []., the quality control of snp data was performed using r software []. snps with missing rate across samples more than 5% and minor allele frequency […]


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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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