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Methods Mol Biol. 2019;1933:265-275. doi: 10.1007/978-1-4939-9045-0_16.

De Novo Plant Transcriptome Assembly and Annotation Using Illumina RNA-Seq Reads.

Author information

1
School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia.
2
New York Genome Center and Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
3
School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia. m.tanurdzic@uq.edu.au.

Abstract

The ability to identify and quantify transcribed sequences from a multitude of organisms using high-throughput RNA sequencing has revolutionized our understanding of genetics and plant biology. However, a number of computational tools used in these analyses still require a reference genome sequence, something that is seldom available for non-model organisms. Computational tools employing de Bruijn graphs to reconstruct full-length transcripts from short sequence reads allow for de novo transcriptome assembly. Here we provide detailed methods for generating and annotating de novo transcriptome assembly from plant RNA-seq data.

KEYWORDS:

De novo transcriptome assembly; Long noncoding RNA; RNA-seq; Trinity

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