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Trinity | Full-length transcriptome assembly from RNA-Seq data without a reference genome

Builds transcriptomes from RNA-seq data. Trinity is a standalone software composed of three main components: (i) Inchworm, that first generates transcript contigs; (ii) Chrysalis, for clustering them and constructing complete de Bruijn graphs for each cluster and; (iii) Butterfly that processes individual graphs in parallel for finally resulting to the reconstruction of the transcript sequences.

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Trinity classification

Trinity specifications

Unique identifier:
Command line interface
Output format:
Programming languages:
C++, Java, Perl, R, Shell (Bash)
Computer skills:
Software type:
Restrictions to use:
Operating system:
BSD 3-clause “New” or “Revised” License
Bowtie, Samtools, R, Blast+

Trinity distribution


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Trinity support



  • Brian Haas <>
  • Aviv Regev <>


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Broad Institute of MIT and Harvard, Cambridge, MA, USA; CSIRO Ecosystem Sciences, Black Mountain Labs, Canberra, ACT, Australia; [etc.]

Funding source(s)

Supported in part by Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No.:HHSN272200900018C, HHMI, an NIH PIONEER award, a Center for Excellence in Genome Science grant 5P50HG006193-02 from the NHGRI and the Klarman Cell Observatory at the Broad Institute (AR), the Commonwealth Scientific and Industrial Research Organization’s (CSIRO) Office of the Chief Executive (OCE), the Clore Foundation, the National Science Foundation grant number OCI-1053575 for the Extreme Science and Engineering Discovery Environment (XSEDE) project, in part by a NIH grant 1R01HG005232-01A1, by Dr. James Thomson’s MacArthur Professorship and by Morgridge Institute for Research support for Computation and Informatics in Biology and Medicine, by the Bundesministerium für Bildung und Forschung (BMBF) via the project ‘NGSgoesHPC’, the Fund for Scientific Research - Flanders (FWO Vlaanderen), Belgium, the National Science Foundation under Grant No. ABI-1062432 and CNS-0521433 to Indiana University, and by Indiana METACyt Initiative.

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