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BroadE: The General Approach to De novo RNA-Seq Assembly Using De Bruijn Graphs

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Published on Oct 8, 2013

Copyright Broad Institute, 2013. All rights reserved.

Trinity, developed at the Broad Institute, 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 videos below describe how Trinity can be leveraged for transcriptome assembly, including an overview of the assembly algorithm, and running Trinity using strand-specific RNA-Seq data. Additional videos are in the works to provide a hands-on tutorial and guide users through downstream analyses such as identifying differentially expressed transcripts.

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