Skip to main content

Introduction to the Trinity Cancer Transcriptome Analysis Toolkit

By Brian Haas1, Aviv Regev, Bill Barnett2

1. Broad Institute 2. Indiana University

Licensed according to this deed.

Published on


This short video provides an overview of our ITCR-funded effort to leverage RNA-Seq and de novo transcriptome assembly to assist researchers in studying cancer transcriptomes. 



Visit our NCGAS Trinity/Galaxy portal to access these compute resources:

Trinity software, tutorials, and documentation are all available from the main Trinity website:


  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 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. PubMed PMID: 21572440.

  • Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11. PubMed PMID: 23845962.

Cite this work

Researchers should cite this work as follows:

  • Brian Haas; Aviv Regev; Bill Barnett (2015), "Introduction to the Trinity Cancer Transcriptome Analysis Toolkit,"

    BibTex | EndNote