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

BMC Genomics
Jialei DuanXiuying Kong

Abstract

Rapid advances in next-generation sequencing methods have provided new opportunities for transcriptome sequencing (RNA-Seq). The unprecedented sequencing depth provided by RNA-Seq makes it a powerful and cost-efficient method for transcriptome study, and it has been widely used in model organisms and non-model organisms to identify and quantify RNA. For non-model organisms lacking well-defined genomes, de novo assembly is typically required for downstream RNA-Seq analyses, including SNP discovery and identification of genes differentially expressed by phenotypes. Although RNA-Seq has been successfully used to sequence many non-model organisms, the results of de novo assembly from short reads can still be improved by using recent bioinformatic developments. In this study, we used 212.6 million pair-end reads, which accounted for 16.2 Gb, to assemble the hexaploid wheat transcriptome. Two state-of-the-art assemblers, Trinity and Trans-ABySS, which use the single and multiple k-mer methods, respectively, were used, and the whole de novo assembly process was divided into the following four steps: pre-assembly, merging different samples, removal of redundancy and scaffolding. We documented every detail of these steps and how these s...Continue Reading

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Feb 4, 2014·BMC Research Notes·Keng-See ChowZainorlina Mohd-Zainuddin
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Related Concepts

Sequence Determinations, RNA
RNA, Plant
Computational Molecular Biology
Expressed Sequence Tags
Gene Expression Profiles
Attention
Genes
Genome
RNA
Wheat (Dietary)

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