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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.


  • 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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