Trinity pipeline

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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Documentation


Maintainers


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

Publications for Trinity

Trinity IN pipelines

 (355)
2018
PMCID: 5739345
PMID: 29091815
DOI: 10.1016/j.phytochem.2017.10.004

[…] using trimmomatic (parameter: leading:10 trailing:10 slidingwindow:4:15 minlen:30) (v0.32, (bolger et al., 2014). only surviving paired-end reads were used to generate de novo assemblies using trinity (v2014-07-17) (grabherr et al., 2011) and only transcripts >250 bp were reported (table 1). the protein sequences of iridoid synthases from catharanthus roseus (afw98981.1) and olea […]

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: 5761878
PMID: 29320569
DOI: 10.1371/journal.pone.0190175

[…] were deposited in the genbank short read archive (accession no. srr5369792)., the raw reads were first filtered to obtain high-quality reads and then assembled de novo into contigs using trinity software [27]. in this step, clean data (clean reads) were obtained by removing reads containing an adaptor and poly (n) sequences, and those of low quality from the raw data. also, 90% […]

2018
PMCID: 5779695
PMID: 29360856
DOI: 10.1371/journal.pone.0191686

[…] recommended protocols. two or three biological replicates for each treatment were prepared., after sequencing, the raw data were filtered against low-quantity reads and adaptor contamination using trinity. clean reads were de novo assembled using trinity with k-mer = 25 [24]. annotations of all the unigenes were performed by a blastx search against the nr, swiss-prot, kog, kegg databases […]

2018
PMCID: 5779695
PMID: 29360856
DOI: 10.1371/journal.pone.0191686

[…] for each treatment were prepared., after sequencing, the raw data were filtered against low-quantity reads and adaptor contamination using trinity. clean reads were de novo assembled using trinity with k-mer = 25 [24]. annotations of all the unigenes were performed by a blastx search against the nr, swiss-prot, kog, kegg databases and pfam with a cut-off e-value of ≤1e-5. we obtained […]

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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