Tools for building de novo transcriptome assembly

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 sam...

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Bibliographic Details
Published in:Current plant biology 2017-09, Vol.11-12 (C), p.41-45
Main Authors: Geniza, Matthew, Jaiswal, Pankaj
Format: Article
Language:English
Subjects:
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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
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Summary: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.
ISSN:2214-6628
2214-6628
DOI:10.1016/j.cpb.2017.12.004