Trinity protocols

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chevron_left Gene prediction Protein-coding gene prediction Alternative splicing events identification Genome assembly Reference-based transcriptome assembly Differential expression De novo transcriptome assembly Gene prediction Normalization chevron_right
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Trinity specifications

Information


Unique identifier OMICS_01327
Name Trinity
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
Requirements
Bowtie, Samtools, R, Blast+
Maintained Yes

Subtools


  • Butterfly
  • Chrysalis
  • Inchworm

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Maintainers


  • person_outline Brian Haas <>
  • person_outline Aviv Regev <>

Publications for Trinity

Trinity in pipelines

 (831)
2018
PMCID: 5753479
PMID: 29298680
DOI: 10.1186/s12864-017-4382-2

[…] - p. formosa: samn06894540 | p. latipinna: samn06894541 | p. mexicana: samn06894542).table 1a: after trimming, a: after trimming, the de novo assembly for the three read sets was conducted with the trinity assembler (table ). the average contig length for the 108,690 transcripts for p. formosa was 1077 bp, for p. latpinna there were 117,211 transcripts with an average length of 1232 bp, […]

2018
PMCID: 5753516
PMID: 29298661
DOI: 10.1186/s12863-017-0592-5

[…] (< 20) and poly-n reads (> 20% reads) in seqprep (https://github.com/jstjohn/seqprep) and sickle (https://github.com/najoshi/sickle). de novo transcriptome assembly was accomplished using trinity (http://trinityrnaseq.sourceforge.net/) [, ]. the gene functions of all assembled unigenes were annotated based on the following databases with nr protein sequences, including swissprot (a […]

2018
PMCID: 5759245
PMID: 29310597
DOI: 10.1186/s12864-017-4379-x

[…] this resulted in high quality rna-seq datasets, which contained between 180 and 210 m paired-end reads for each of the four species (table ).table 1, the initial de novo assemblies generated from trinity ranged between 200,760 and 242,899 transcripts greater than 297 bp in length for the four species (table ). as a preliminary assessment of assembly quality, prior to filtering, we mapped […]

2018
PMCID: 5759245
PMID: 29310597
DOI: 10.1186/s12864-017-4379-x

[…] distribution size of the current salmon assembly (at all four filtering steps: unfiltered, after transdecoder single-best orf prediction, after cd-hit clustering at 100% identity and after trinity full-length transcript analysis (e.g. final version)) against the ncbi atlantic salmon refseq proteins. given the high quality of the recently published protein set for atlantic salmon, […]

2018
PMCID: 5760653
PMID: 29317769
DOI: 10.1038/s41598-017-18432-5

[…] in which more than 10% of the bases had q-values < 20. sequences shorter than 60 bp as well as rrna sequences that aligned with the silva database were discarded to avoid sequencing artifacts. trinity was then used to separately assemble the left reads into the resulting contigs for each sample, and the contigs were joined into transcripts. transcripts longer than 200 bp were selected […]

Trinity in publications

 (4690)
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. […]

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

[…] instar and an adult female. among the different instars, the closer the stages, the higher the similarity of transcripts profiles., qrt-pcr analyses were performed on ten randomly selected genes: trinity_dn6817_c0_g2, trinity_dn5360_c0_g1, trinity_dn25340_c3_g1, trinity_dn22738_c0_g1, trinity_dn11167_c0_g1, trinity_dn62673_c0_g1, trinity_dn35383_c0_g1, trinity_dn2037_c0_g2, […]

PMCID: 5952850
PMID: 29785177
DOI: 10.1186/s41065-018-0060-x

[…] hiseq™2000(illumina)., seqpreq (https://github.com/jstjohn/seqprep)and sickle (https://github.com/najoshi/sickle) were used to remove sequencing adapters and trim low-quality sequences. after that, trinity [] software was used to assemble all clean high-quality reads. the expression level of transcripts was measured by rsem, and the result was reported by units of tpm (transcripts per […]

PMCID: 5949330
PMID: 29756296
DOI: 10.14814/phy2.13705

[…] were excluded from participation. participants provided written informed consent prior to participation. all studies were approved by the faculty of health science research ethics committee (trinity college dublin) and conducted in accordance with the declaration of helsinki (2008)., prior to exercise testing, each participant was assessed for bmi and waist‐to‐hip ratio, provided […]

PMCID: 5945717
PMID: 29748592
DOI: 10.1038/s41598-018-25867-x

[…] (hokkaido system science inc., hokkaido, japan; sequencing team of kakenhi 221s0002 in tokyo university, kashiwa, japan). cleaned sequence reads were assembled into contigs (is-transcripts) by trinity (version 2013-11-10; https://github.com/trinityrnaseq/trinityrnaseq/wiki; trinity.pl–seqtype fq–jm 196 g–left $read_file_1.fastq–right $read_file_2.fastq–cpu 30–min_kmer_cov 2–output […]

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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