TY - JOUR KW - BinPacker KW - CD-HIT-ES KW - De novo assembly KW - de novo transcriptome assembly KW - Differential gene expression KW - Gene expression KW - Gene Ontology KW - Genetic marker identification KW - Genome annotation KW - Plant gene expression KW - Plant Ontology KW - Plant Reactome KW - RNA QUAST KW - RNA-Seq KW - SPAdes KW - Transcriptiome KW - TransRate KW - Trinity KW - Velvet Oases AU - Matthew Geniza AU - Pankaj Jaiswal AB - 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. BT - Current Plant Biology DO - https://doi.org/10.1016/j.cpb.2017.12.004 N1 - Genomic resources and databases N2 - 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. PY - 2017 SP - 41 EP - 45 T2 - Current Plant Biology TI - Tools for building de novo transcriptome assembly UR - http://www.sciencedirect.com/science/article/pii/S2214662817301032 VL - 11-12 SN - 2214-6628 ER -