trinotate
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'trinotate' Versions
- 3.2.2
Link to section 'Commands' of 'trinotate' 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
Link to section 'Module' of 'trinotate' Module
You can load the modules by:
module load biocontainers
module load trinotate
Link to section 'Example job' of 'trinotate' Example job
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