Genome-guided transcriptome assembly in the age of next-generation sequencing

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1234-40. doi: 10.1109/tcbb.2013.140.


Next-generation sequencing technologies provide unprecedented power to explore the repertoire of genes and their alternative splice variants, collectively defining the transcriptome of a species in great detail. However, assembling the short reads into full-length gene and transcript models presents significant computational challenges. We review current algorithms for assembling transcripts and genes from next-generation sequencing reads aligned to a reference genome, and lay out areas for future improvements.

Publication types

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

MeSH terms

  • Algorithms*
  • Base Sequence
  • Chromosome Mapping / methods*
  • Computer Simulation
  • Genome / genetics*
  • Models, Genetic*
  • Molecular Sequence Data
  • Sequence Analysis, RNA / methods*
  • Transcriptome / genetics*