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Trinity specifications


Unique identifier OMICS_01327
Name Trinity
Alternative name trinityrnaseq
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTQ, BAM
Output format FASTA
Operating system Unix/Linux
Programming languages C++, Java, Perl, R, Shell (Bash)
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 2.5.1
Stability Stable
Bowtie, Samtools, R, Blast+
Maintained Yes


  • Butterfly
  • Chrysalis
  • Inchworm




No version available



  • person_outline Brian Haas
  • person_outline Aviv Regev

Publications for Trinity

Trinity citations


Multiple origins of green blood in New Guinea lizards

Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] remove adapters (, ), yielding an average of 8,504,473 reads (302,468 to 119,426,985) and 1,141,548,626 bp (42,543,058 to 17,007,264,440) per sample. Filtered reads were assembled into contigs using Trinity (). To check for contamination, all contigs were aligned to the nonredundant protein database by BLASTP with an e value cutoff of 1 × 10−6 and checked for best hits to squamate reptiles. We al […]


De novo characterization of Phenacoccus solenopsis transcriptome and analysis of gene expression profiling during development and hormone biosynthesis

Sci Rep
PMCID: 5954142
PMID: 29765069
DOI: 10.1038/s41598-018-25845-3

[…] EggI, second, third and adult female) of P. solenopsis. The de-novo assembly of short read sequence without having reference genome poses a challenge with existing bioinformatics tools. Here, we used trinity software which is a well-accepted methodology for its precision and quality of the assembled sequences. Before doing assembly, the four datasets (EggI, second, third instar and adult female) w […]


Identification of genes regulating ovary differentiation after pollination in hazel by comparative transcriptome analysis

BMC Plant Biol
PMCID: 5941469
PMID: 29739322
DOI: 10.1186/s12870-018-1296-3
call_split See protocol

[…] 5% unknown bases (N), and low quality reads (defined as reads in which the proportion of bases with a quality score < 10 was greater than 20%), the remaining clean reads were stored in FASTQ format. Trinity (version: v2.0.6) [] was used to perform de novo assembly with clean reads from all 12 libraries with min_contig_length set to 150 and min_kmer_cov set to 3 and all other parameters set to def […]


Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasia are determined largely by Symbiodinium

PMCID: 5941691
PMID: 29739445
DOI: 10.1186/s40168-018-0465-9

[…] e detected later using BLAST.) The Aiptasia-originated reads from all samples were quality trimmed with Trimmomatic (parameters: LEADING:5 TRAILING:5 MINLEN:36), merged, and a de novo assembled using Trinity []. After excluding reads of < 200 bp, the resulting assembly contained 359,881 transcripts and is hereafter designated as the “Aiptasia transcriptome”. Profile expression reads from each samp […]


The aquatic animals’ transcriptome resource for comparative functional analysis

BMC Genomics
PMCID: 5954267
PMID: 29764375
DOI: 10.1186/s12864-018-4463-x

[…] llustrated in Fig. and further detail is provided in the Materials and Methods section. First, we optimized the de novo assembly pipeline of RNA-seq data [] by combining Oases, SOAPdenovo-Trans, and Trinity assemblers. To obtain complete transcriptomes from various assemblers [, ], we used the CD-HIT-EST cluster tool to merge Oases, SOAPdenovo-Trans, and Trinity assembling results. This combinati […]


Transcriptome sequencing and analysis during seed growth and development in Euryale ferox Salisb

BMC Genomics
PMCID: 5944168
PMID: 29743016
DOI: 10.1186/s12864-018-4707-9

[…] analysis has become more efficient and cost-effective. Liu et al. [] reported that 51,792 unigenes with an average length of 849 bp and an N50 length of 1448 bp were obtained from lettuce seed using Trinity assembly software. Yin et al. [] assembled 59,236 unigenes with a mean length of 751 bp and an N50 length of 1130 bp from transcriptome sequencing of peanut seed. In the present study, the N50 […]


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