Tools for building de novo transcriptome assembly

TitleTools for building de novo transcriptome assembly
Publication TypeJournal Article
Year of Publication2017
AuthorsGeniza, M, Jaiswal, P
JournalCurrent Plant Biology
Pagination41 - 45
KeywordsBinPacker, CD-HIT-ES, De novo assembly, de novo transcriptome assembly, Differential gene expression, Gene Expression, Gene Ontology, Genetic marker identification, Genome annotation, Plant gene expression, Plant Ontology, Plant Reactome, RNA QUAST, RNA-Seq, SPAdes, Transcriptiome, TransRate, Trinity, Velvet Oases

The availability of RNA-Seq method allows researchers to capture the spatial or temporal profile of transcriptomes from various types of biological samples. Expression atlas view of maize genes 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.