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Nat Protoc DOI:10.1038/nprot.2013.084

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

Publication TypeJournal Article
Year of Publication2013
AuthorsHaas, BJ, Papanicolaou, A, Yassour, M, Grabherr, M, Blood, PD, Bowden, J, Couger, MBrian, 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
JournalNat Protoc
Date Published2013 Aug
KeywordsBase Sequence, Gene Expression Profiling, RNA, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Sequence Analysis, RNA, Software, Transcriptome

De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.


Alternate JournalNat Protoc
PubMed ID23845962
PubMed Central IDPMC3875132
Grant ListHHSN272200900018C / AI / NIAID NIH HHS / United States
1R01HG005232-01A1 / HG / NHGRI NIH HHS / United States
P50 HG006193 / HG / NHGRI NIH HHS / United States
HHSN272200900018C / / PHS HHS / United States
5P50HG006193-02 / HG / NHGRI NIH HHS / United States
/ / Howard Hughes Medical Institute / United States
R01 HG005232 / HG / NHGRI NIH HHS / United States