Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering

Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

(2013) Fei Lu et al.   PLoS Genetics

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

Genome-wide association genetics of an adaptive trait in lodgepole pine

(2012) THOMAS L. PARCHMAN et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

The draft genome of a diploid cotton Gossypium raimondii

(2012) Kunbo Wang et al.   NATURE GENETICS

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

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

SEED: efficient clustering of next-generation sequences

(2011) Ergude Bao et al.   BIOINFORMATICS

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

(2011) PAUL A. HOHENLOHE et al.   Molecular Ecology Resources

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

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

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

(2011) Paul D. Etter et al.   PLoS One

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

SlideSort: all pairs similarity search for short reads

(2010) Kana Shimizu et al.   BIOINFORMATICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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