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.
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