Trinity is a tool for de novo transcriptome assembly of RNA-seq data and consists of three modules: Inchworm, Chrysalis, and Butterfly. The algorithm uses de Bruijn graphs, dynamic programming method, it can detect isoforms, handle paired-end reads, multiple insert sizes, and strandedness. The running time is exponential related to the number of graph branches.
Transcriptomics; Gene expression; Gene transcripts
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. https://doi.org/10.1038/nbt.1883
PMID: 21572440
PMCID: PMC3571712
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. https://doi.org/10.1038/nprot.2013.084
PMID: 23845962
PMCID: PMC3875132
Henschel R, Lieber M, Wu L, Nista, PM, Haas BJ, LeDuc R "Trinity RNA-Seq assembler performance optimization" XSEDE 2012 Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond. https://doi.org/10.1145/2335755.2335842
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