HPC Module: Trinity
Synopsis
Adds Trinity software to your environment.
| About This Software | |
|---|---|
| Official Site | https://github.com/trinityrnaseq/trinityrnaseq/wiki |
| Tags | RNA, Inchwork, Chrysalis, Butterfly, De Novo Reconstruction, Transcription |
Installed Versions
| Version | Install Date | Default? |
|---|---|---|
| 2.1.1 | 2019-11-11 | |
| 2.2.0 | 2019-11-11 |
Description
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. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads.
Citation(s)
Trinity can be referenced as:
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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. Protocol for using Trinity for de novo transcriptome assembly and downstream analyses:
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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. Open Access in PMC doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11. PubMed PMID:23845962. Performance tuning of Trinity is described in:
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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. ISBN: 978-1-4503-1602-6 doi: 10.1145/2335755.2335842.
Category
| Library | Programming | Software | SysAdmin |
|---|---|---|---|