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:
Home page: https://github.com/Trinotate/Trinotate.github.io/blob/master/index.asciidoc

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

3.2.2

BELL

3.2.2

GAUTSCHI

3.2.2

NEGISHI

3.2.2

SCHOLAR

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 -p wholenode        # Partition 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
module biocontainers trinotate

# Your trinotate workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers trinotate

# Your trinotate workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers trinotate

# Your trinotate workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers trinotate

# Your trinotate workflow...

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers trinotate

# Your trinotate workflow...