A high-throughput SNP discovery strategy for RNA-seq data

Genomics of the origin and evolution of Citrus

(2018) Guohong Albert Wu et al.   NATURE

Trends in plant research using molecular markers

(2017) Jose Antonio Garrido-Cardenas et al.   PLANTA

Differential Sensitivity of Fruit Pigmentation to Ultraviolet Light between Two Peach Cultivars

(2017) Yun Zhao et al.   Frontiers in Plant Science

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

(2016) Arthur T. O. Melo et al.   BMC BIOINFORMATICS

Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

(2015) Guiyan Ni et al.   BMC GENOMICS

Distinct Carotenoid and Flavonoid Accumulation in a Spontaneous Mutant of Ponkan (Citrus reticulata Blanco) Results in Yellowish Fruit and Enhanced Postharvest Resistance

(2015) Tao Luo et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing

(2014) Yang Yu et al.   PLoS One

OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data

(2014) Pengyuan Zhu et al.   PLoS One

The Impacts of Read Length and Transcriptome Complexity for De Novo Assembly: A Simulation Study

(2014) Zheng Chang et al.   PLoS One

The complex transcriptional landscape of the anucleate human platelet

(2013) Paul F Bray et al.   BMC GENOMICS

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

(2013) Emma M. Quinn et al.   PLoS One

SNP calling using genotype model selection on high-throughput sequencing data

(2012) Na You et al.   BIOINFORMATICS

Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes

(2012) Pavana J. Hiremath et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2012) Rasmus Nielsen et al.   PLoS One

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

(2012) Osvaldo Zagordi et al.   PLoS One

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

(2011) J. E. SEEB et al.   Molecular Ecology Resources

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

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

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

Novel Tools for Conservation Genomics: Comparing Two High-Throughput Approaches for SNP Discovery in the Transcriptome of the European Hake

(2011) Ilaria Milano et al.   PLoS One

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Single-Nucleotide Polymorphism Genotyping in Mapping Populations via Genomic Reduction and Next-Generation Sequencing: Proof of Concept

(2010) Peter J. Maughan et al.   Plant Genome

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

De novo fragment assembly with short mate-paired reads: Does the read length matter?

(2008) M. J. Chaisson et al.   GENOME RESEARCH

Characterization of cDNAs associated with lignification and their expression profiles in loquat fruit with different lignin accumulation

(2008) Lan Lan Shan et al.   PLANTA