Full-length Transcriptome Assembly From RNA-Seq Data Without a Reference Genome

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

Abstract

Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.

Publication types

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

MeSH terms

  • Algorithms*
  • Base Sequence
  • Gene Expression Profiling / methods*
  • Molecular Sequence Data
  • RNA / chemistry*
  • RNA / genetics*
  • Reference Values
  • Sequence Analysis, RNA / methods*
  • Sequence Analysis, RNA / standards
  • Transcriptome

Substances

  • RNA

Associated data

  • GEO/GSE29209