Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology

A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication

(2014) Wataru Kai et al.   BMC GENOMICS

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

Recent novel approaches for population genomics data analysis

(2014) Kimberly R. Andrews et al.   MOLECULAR ECOLOGY

Genetic and life-history changes associated with fisheries-induced population collapse

(2013) Lilian Pukk et al.   Evolutionary Applications

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

(2013) R. Ogden et al.   MOLECULAR ECOLOGY

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

RAD-Seq derived markers flank the shell colour and banding loci of theCepaea nemoralissupergene

(2013) Paul M. Richards et al.   MOLECULAR ECOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley

(2013) Martin Mascher et al.   PLoS One

Double-restriction-site-associated DNA (dRAD) approach for fast microsatellite marker development in Eurasian perch (Perca fluviatilis L.)

(2013) Lilian Pukk et al.   Conservation Genetics Resources

Multiplex target capture with double-stranded DNA probes

(2013) Peidong Shen et al.   Genome Medicine

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

(2013) Lauren M. Bragg et al.   PLoS Computational Biology

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

(2012) Huaan Yang et al.   BMC GENOMICS

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

Progress in Ion Torrent semiconductor chip based sequencing

(2012) Barry Merriman et al.   ELECTROPHORESIS

Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes

(2012) I. Keller et al.   MOLECULAR ECOLOGY

Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach

(2012) Matthieu Bruneaux et al.   MOLECULAR ECOLOGY

Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish(Coregonus clupeaformis)

(2012) Pierre-Alexandre Gagnaire et al.   MOLECULAR ECOLOGY

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant

(2012) Reeta Sharma et al.   PLoS One

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

(2011) Simon W. Baxter et al.   PLoS One

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

(2010) David L Hyten et al.   BMC GENOMICS

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One