Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.
The Broad Institute, Cambridge, MA
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Manfred G. Grabherr, Brian J. Haas, […], and Aviv Regev
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
Nat Biotechnol. 2011 May 15; 29(7): 644–652. doi: 10.1038/nbt.1883