Next-generation transcriptome assembly

Nat Rev Genet. 2011 Sep 7;12(10):671-82. doi: 10.1038/nrg3068.


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Animals
  • Base Sequence
  • Cloning, Molecular
  • Gene Expression Profiling / methods
  • Gene Expression Profiling / trends*
  • Gene Library
  • Humans
  • Models, Biological
  • Molecular Sequence Annotation / methods
  • Molecular Sequence Annotation / trends
  • Molecular Sequence Data
  • Sequence Analysis, DNA / methods
  • Sequence Analysis, DNA / trends
  • Sequence Analysis, RNA / methods
  • Sequence Analysis, RNA / trends