Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical andin silicooptimization in tomato

Progress, challenges and the future of crop genomes

(2015) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations

(2015) Josh Clevenger et al.   Molecular Plant

Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato

(2015) Kenta Shirasawa et al.   PLANT BIOTECHNOLOGY JOURNAL

Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations

(2014) Maria Ercolano et al.   BMC GENOMICS

Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

(2014) et al.   PLANT JOURNAL

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

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

Fluorescence In Situ Hybridization and Optical Mapping to Correct Scaffold Arrangement in the Tomato Genome

(2014) Lindsay A. Shearer et al.   G3-Genes Genomes Genetics

DNA marker applications to molecular genetics and genomics in tomato

(2013) Kenta Shirasawa et al.   BREEDING SCIENCE

Genome-Wide Association Studies Using Single Nucleotide Polymorphism Markers Developed by Re-Sequencing of the Genomes of Cultivated Tomato

(2013) K. Shirasawa et al.   DNA RESEARCH

Genome-Wide SNP Genotyping to Infer the Effects on Gene Functions in Tomato

(2013) H. Hirakawa et al.   DNA RESEARCH

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Genotyping-by-Sequencing for Plant Breeding and Genetics

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

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

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Array-based high-throughput DNA markers for crop improvement

(2008) P K Gupta et al.   HEREDITY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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