Trinotate

Introduction

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

For more information, please check its website: https://biocontainers.pro/tools/trinotate and its home page on Github.

Versions

  • 3.2.2

Commands

  • Trinotate

  • Build_Trinotate_Boilerplate_SQLite_db.pl

  • EMBL_dat_to_Trinotate_sqlite_resourceDB.pl

  • EMBL_swissprot_parser.pl

  • PFAM_dat_parser.pl

  • PFAMtoGoParser.pl

  • RnammerTranscriptome.pl

  • TrinotateSeqLoader.pl

  • Trinotate_BLAST_loader.pl

  • Trinotate_GO_to_SLIM.pl

  • Trinotate_GTF_loader.pl

  • Trinotate_GTF_or_GFF3_annot_prep.pl

  • Trinotate_PFAM_loader.pl

  • Trinotate_RNAMMER_loader.pl

  • Trinotate_SIGNALP_loader.pl

  • Trinotate_TMHMM_loader.pl

  • Trinotate_get_feature_name_encoding_attributes.pl

  • Trinotate_report_writer.pl

  • assign_eggnog_funccats.pl

  • autoTrinotate.pl

  • build_DE_cache_tables.pl

  • cleanMe.pl

  • cleanme.pl

  • count_table_fields.pl

  • create_clusters_tables.pl

  • extract_GO_assignments_from_Trinotate_xls.pl

  • extract_GO_for_BiNGO.pl

  • extract_specific_genes_from_all_matrices.pl

  • import_DE_results.pl

  • import_Trinotate_xls_as_annot.pl

  • import_expression_and_DE_results.pl

  • import_expression_matrix.pl

  • import_samples_n_expression_matrix.pl

  • import_samples_only.pl

  • import_transcript_annotations.pl

  • import_transcript_clusters.pl

  • import_transcript_names.pl

  • init_Trinotate_sqlite_db.pl

  • legacy_blast.pl

  • make_cXp_html.pl

  • obo_tab_to_sqlite_db.pl

  • obo_to_tab.pl

  • prep_nuc_prot_set_for_trinotate_loading.pl

  • print.pl

  • rnammer_supperscaffold_gff_to_indiv_transcripts.pl

  • runMe.pl

  • run_TrinotateWebserver.pl

  • run_cluster_functional_enrichment_analysis.pl

  • shrink_db.pl

  • sqlite.pl

  • superScaffoldGenerator.pl

  • test_Barplot.pl

  • test_GO_DAG.pl

  • test_GenomeBrowser.pl

  • test_Heatmap.pl

  • test_Lineplot.pl

  • test_Piechart.pl

  • test_Scatter2D.pl

  • test_Sunburst.pl

  • trinotate_report_summary.pl

  • update_blastdb.pl

  • update_seq_n_annotation_fields.pl

Module

You can load the modules by:

module load biocontainers
module load trinotate

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Trinotate on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=trinotate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers trinotate

sqlite_db="myTrinotate.sqlite"

Trinotate ${sqlite_db} init \
    --gene_trans_map data/Trinity.fasta.gene_to_trans_map \
    --transcript_fasta data/Trinity.fasta \
     --transdecoder_pep \
    data/Trinity.fasta.transdecoder.pep

Trinotate ${sqlite_db} LOAD_swissprot_blastp data/swissprot.blastp.outfmt6

Trinotate ${sqlite_db} LOAD_pfam data/TrinotatePFAM.out