Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes

Frontiers in Genetics
Joanna MoretonRichard D Emes

Abstract

De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome. Transcriptomics allows the understanding and comparison of spatial and temporal samples within an organism, and allows surveying of multiple individuals or closely related species. De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome. It also allows the discovery of alternate splice forms of coding RNAs and also non-coding RNAs, which are often missed by proteomic approaches, or are incompletely annotated in genome studies. The limitations of the method are that the generation of a truly complete assembly is unlikely, and so we require some methods for the assessment of the quality and appropriateness of a generated transcriptome. Whilst no single consensus pipeline or tool is agreed as optimal, various algorithms, and easy to use software do exist making transcriptome generation a more common approach. With this expansion of data, questions still exist rel...Continue Reading

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Methods Mentioned

BETA
the
454 sequencing

Software Mentioned

Rockhopper
Trinity assembler
EVAL
DESeq2
RSEM
REF
Trinity
afterParty
BLAST
CEGMA

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