Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.)

(2012) Jianan Zhang et al.   BMC GENOMICS

Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq

(2012) Chao Feng et al.   BMC GENOMICS

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat

(2012) Martin Trick et al.   BMC PLANT BIOLOGY

Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence

(2011) Dario Cantu et al.   BMC GENOMICS

De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants

(2011) Rob W Ness et al.   BMC GENOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Cell Walls of Developing Wheat Starchy Endosperm: Comparison of Composition and RNA-Seq Transcriptome

(2011) T. K. Pellny et al.   PLANT PHYSIOLOGY

Transcriptome Analysis of H2O2-Treated Wheat Seedlings Reveals a H2O2-Responsive Fatty Acid Desaturase Gene Participating in Powdery Mildew Resistance

(2011) Aili Li et al.   PLoS One

RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.)

(2011) Caroline Pont et al.   GENOME BIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

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

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

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

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

Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing

(2009) Peter C. Bundock et al.   PLANT BIOTECHNOLOGY JOURNAL

TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics

(2009) K. Mochida et al.   PLANT PHYSIOLOGY