Nature Reviews Genetics 12, 671-682 (October 2011) | doi:10.1038/nrg3068

Article series: Study designs

Next-generation transcriptome assembly

Jeffrey A. Martin1 & Zhong Wang1  About the authors


Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches — reference-based, de novo and combined strategies — along with some perspectives on transcriptome assembly in the near future.

Author affiliations

  1. Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, 2800 Mitchell Drive, MS100 Walnut Creek, California 94598, USA.

Correspondence to: Jeffrey A. Martin1 Email:

Correspondence to: Zhong Wang1 Email:

Published online 7 September 2011