Tools for building de novo transcriptome assembly

Abstract

The availability of RNA-Seq method allows researchers to capture the spatial or temporal profile of transcriptomes from various types of biological samples. The transcriptome data from a species can be analyzed in the context of its sequenced genomes or closely related genome to score biological sample-specific transcript isoforms, novel transcribed regions and to refine gene models including identification of new genes, in addition to the differential gene expression analysis. However, many plant species of importance currently lack a sequenced genome or a closely related reference genome and thus, rely on the de novo methods for generating transcript models and transcriptome assemblies. Here we describe various tools used for de novo transcriptome assembly and discuss the data management practices and standards.

Keywords

• Transcriptiome
• De novo assembly
• Gene expression
• RNA-Seq
• Differential gene expression
• Plant gene expression
• Plant Ontology
• Gene Ontology
• De novo transcriptome assembly
• Genome annotation
• Genetic marker identification
• Plant Reactome
• Velvet Oases
• SPAdes
• Trinity
• BinPacker
• RNA QUAST
• TransRate
• CD-HIT-ES