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

Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

(2016) Chunfa Tong et al.   PLoS One

High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

(2015) Wellington Muchero et al.   BMC GENOMICS

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

(2015) Janna L. Fierst   Frontiers in Genetics

Molecular Mapping of Restriction-Site Associated DNA Markers in Allotetraploid Upland Cotton

(2015) Yangkun Wang et al.   PLoS One

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

High-resolution genetic maps ofEucalyptusimproveEucalyptus grandisgenome assembly

(2014) Jérôme Bartholomé et al.   NEW PHYTOLOGIST

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)

(2013) Ryo Kakioka et al.   BMC GENOMICS

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing

(2013) Xiaowen Sun et al.   PLoS One

Genomic insights into salt adaptation in a desert poplar

(2013) Tao Ma et al.   Nature Communications

Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads

(2012) Z. Chong et al.   BIOINFORMATICS

A reference linkage map for Eucalyptus

(2012) Corey J Hudson et al.   BMC GENOMICS

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

(2012) Nian Wang et al.   BMC PLANT BIOLOGY

Special features of RAD Sequencing data: implications for genotyping

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Paired-end RAD-seq for de novo assembly and marker design without available reference

(2011) Eva-Maria Willing et al.   BIOINFORMATICS

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

(2011) Yada Chutimanitsakun et al.   BMC GENOMICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Forest tree genomics: growing resources and applications

(2011) David B. Neale 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

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

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

Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne

(2011) W. F. Pfender et al.   THEORETICAL AND APPLIED GENETICS

High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus

(2010) Sofia Berlin et al.   BMC GENOMICS

A hidden Markov model approach to multilocus linkage analysis in a full-sib family

(2010) Chunfa Tong et al.   Tree Genetics & Genomes

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Detection of quantitative trait loci influencing growth trajectories of adventitious roots in Populus using functional mapping

(2009) Bo Zhang et al.   Tree Genetics & Genomes

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Genome structure and emerging evidence of an incipient sex chromosome in Populus

(2008) T. Yin et al.   GENOME RESEARCH

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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