Trinotate pipeline

Trinotate specifications


Unique identifier OMICS_19343
Name Trinotate
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0.2
Stability Stable
Requirements TransDecoder, sqlite, NCBI BLAST+, HMMER/PFAM Protein Domain Identification
Source code URL
Maintained Yes


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Trinotate citations

PMCID: 5830717

[…] controlling for differences in sequencing depth among samples by scaling raw counts to counts per million., we used the trinotate pipeline to generate functional annotations for our contigs [74]. trinotate integrates, among others, blast [75] and gene ontology (go) [76] tools. we used the resulting functional information to perform go term enrichment analyses on selected contig sets using […]

PMCID: 5816582

[…] using a bonferroni correction to account false discovery across multiple tests. all analyses were performed using r (version 3.3.2)., the functional annotation of transcripts was based on the trinotate pipeline (version 3.0.1). we matched microarray probe sequences to known sequences using blast against the swissprot annotated database (apweiler et al., 2004), identified protein sequence […]

PMCID: 5513917

[…] using bowtie2 (langmead and salzberg, 2012) and transcript abundance calculated using the rna-seq by expectation maximization (rsem) method (li and dewey, 2011). transcripts were annotated in trinotate v3.0 using blast searches (e value < 10-20) against swissprot. dgea was carried out on the annotated transcripts using the edger package (robinson et al., 2010; mccarthy et al., 2012) […]

PMCID: 4956038

[…] using an illumina paired-end sequencing platform. sequences were then assembled using trinity, a de novo assembly software [5]. more than 145 thousand genes were generated and annotated using the trinotate pipeline ( and blast2go [16]. our aim was to provide the first inclusive annotated transcriptome of c. maculatus. we also assess the degree […]

PMCID: 4473991

[…] unigenes, 30 539 unigenes (67.3%) were annotated through a blastx search with e-values ≤1e–3 (table 2). functional classifications of gene ontology (go) terms of all unigenes were performed using trinotate (quevillon et al., 2005). figure 2 shows enriched go terms for the top 1000 highly expressed transcripts. from our annotated unigenes, 16 were identified as tpss that were more than 500bp. […]

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