GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm

(2015) Boyi Wang et al.   Horticulture Research

Classification and Characterization of Species within the Genus Lens Using Genotyping-by-Sequencing (GBS)

(2015) Melissa M. L. Wong et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Assessment of genetic variation within a global collection of lentil (Lens culinarisMedik.) cultivars and landraces using SNP markers

(2014) Maria Lombardi et al.   BMC GENETICS

Reference-free SNP detection: dealing with the data deluge

(2014) Richard M Leggett et al.   BMC GENOMICS

Estimating genotype error rates from high-coverage next-generation sequence data

(2014) Jeffrey D. Wall et al.   GENOME RESEARCH

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

(2014) Jeffrey C. Glaubitz et al.   PLoS One

Identification of Pummelo Cultivars by Using a Panel of 25 Selected SNPs and 12 DNA Segments

(2014) Bo Wu et al.   PLoS One

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Genetic diversity analysis of yellow mustard (Sinapis alba L.) germplasm based on genotyping by sequencing

(2013) Yong-Bi Fu et al.   GENETIC RESOURCES AND CROP EVOLUTION

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Feeding the future

(2013) Susan McCouch et al.   NATURE

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

(2013) D. I. Lou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Fei Lu et al.   PLoS Genetics

An analysis of consumer demand for fruits in Sri Lanka. 1981–2010

(2012) Jeevika Weerahewa et al.   APPETITE

The effect of strand bias in Illumina short-read sequencing data

(2012) Yan Guo et al.   BMC GENOMICS

Application of Genomic Tools in Plant Breeding

(2012) A. M. Perez-de-Castro et al.   CURRENT GENOMICS

Can genomics boost productivity of orphan crops?

(2012) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

(2012) Jesse A. Poland et al.   PLoS One

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

(2012) Jesse Poland et al.   Plant Genome

Agroecologically efficient agricultural systems for smallholder farmers: contributions to food sovereignty

(2011) Miguel A. Altieri et al.   Agronomy for Sustainable Development

The potential for underutilized crops to improve security of food production

(2011) S. Mayes et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Breeding Technologies to Increase Crop Production in a Changing World

(2010) M. Tester et al.   SCIENCE

Food Security: The Challenge of Feeding 9 Billion People

(2010) H. C. J. Godfray et al.   SCIENCE

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

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH