Skip to main content
The NCI Community Hub will be retiring in May 2024. For more information please visit the NCIHub Retirement Page:

Trinity: RNA-Seq De novo Assembly Application

By Grabherr MG, Brian Haas1, 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

1. Broad Institute

Published on



Quick Guide for the Impatient

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Download Trinity here.

Build Trinity by typing make : ; in the base installation directory.

Assemble RNA-Seq data like so:

Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G

Find assembled transcripts as: trinity_out_dir/trinity.fasta

 : ;

Trinity on Galaxy

In a collaboration between the Broad Institute and Indiana University, we are making Trinity and cancer transcriptome targeted applications available to researchers via our Trinity/NCGAS Galaxy Portal

User Forum

Join the Trinity User Forum

Intro to Trinity

"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. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Briefly, the process works like so:

  • Inchworm assembles the RNA-seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.

  • Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs.

  • Butterfly then processes the individual graphs in parallel, tracing the paths that reads and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that corresponds to paralogous genes."


Have a question - ask us


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.

Cite this work

Researchers should cite this work as follows:

  • Grabherr MG; Brian Haas; 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 (2015), "Trinity: RNA-Seq De novo Assembly Application,"

    BibTex | EndNote