Trinotate 3.2.2

2022-03-17 247 words 2 minutes

Trinotate

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.

Location and version:

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$ which Trinotate
/local/cluster/bin/Trinotate

Example configuration file:

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/local/cluster/Trinotate-3.2.2/auto/conf.txt

Database location:

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/nfs1/CGRB/databases/Trinotate/latest

help message:

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$ Trinotate --help


   usage: /local/cluster/bin/Trinotate <sqlite.db> <command> <input> [...]


     <commands>:

         * Initial import of transcriptome and protein data:

             init --gene_trans_map <file> --transcript_fasta <file> --transdecoder_pep <file>

         * Transdecoder protein search results:

             LOAD_swissprot_blastp <file>
             LOAD_pfam <file>
             LOAD_tmhmm <file>
             LOAD_signalp <file>

          * Trinity transcript search results:

             LOAD_swissprot_blastx <file>
             LOAD_rnammer <file>


          * Load custom blast results using any searchable database


             LOAD_custom_blast --outfmt6 <file> --prog <blastp|blastx> --dbtype <database_name>


          * report generation:

             report [ -E (default: 1e-5) ] [--pfam_cutoff DNC|DGC|DTC|SNC|SGC|STC (default: DNC=domain noise cutoff)]

software ref: https://github.com/Trinotate/Trinotate.github.io/wiki
research ref: https://doi.org/10.1016/j.celrep.2016.12.063