Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Workflow

• Compress data (inchworm)
  • Cut reads into k-mers (k consecutive nucleotides)
  • Overlap and extend
  • Report all sequences
• Build de Bruijn graph (chrysalis)
  • Collect all contigs that share k-1-mers
  • Build graph
  • Map reads to components
• Eumuerate all consistent possibilities (butterfly)
  • Unwrap graph into linear sequences
  • Use reads and pairs to eliminate false sequences
  • Dynamic programming

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