bacterial_genome_annotation/main
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Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| AMRFinderPlus database | AMRFinderPlus database | Select a database to annotate AMR genes with Bakta. |
|
| Bacterial genome annotation database | Bacterial genome annotation database | Select a database to predict CDS and small proteins (sORF) with Bakta. |
|
| Input sequence fasta | Input sequence fasta | Can be any fasta file. |
|
| Plasmid detection database | Plasmid detection database | Select a database to identify plasmids with PlasmidFinder. |
|
| Run Bakta | Run Bakta | Choose if you want to run bakta or not (can take a long time) |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | ISEScan for insertion sequence elements detection | genomic_annotation_insertionelement_isescan toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.3+galaxy0 |
| 6 | Integron Finder for integrons detection | genomic_annotation_integron toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0 |
| 7 | PlasmidFinder for plasmid detection | genomic_annotation_plasmid_plasmidfinder toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 |
| 8 | Bakta functionnal annotation | toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy1 |
| 9 | ToolDistillator without bakta | ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0 |
| 10 | Pick the main bakta file if the tool is run. | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 11 | ToolDistillator summarize without bakta | ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0 |
| 12 | ToolDistillator bakta | ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0 |
| 13 | ToolDistillator summarize bakta | ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| isescan_logfile_text | isescan_logfile_text | n/a |
|
| isescan_orf_faa | isescan_orf_faa | n/a |
|
| isescan_is_fasta | isescan_is_fasta | n/a |
|
| isescan_results_tabular | isescan_results_tabular | n/a |
|
| isescan_orf_fasta | isescan_orf_fasta | n/a |
|
| isescan_summary_tabular | isescan_summary_tabular | n/a |
|
| isescan_annotation_gff3 | isescan_annotation_gff3 | n/a |
|
| integronfinder2_results_tabular | integronfinder2_results_tabular | n/a |
|
| integronfinder2_logfile_text | integronfinder2_logfile_text | n/a |
|
| integronfinder2_summary | integronfinder2_summary | n/a |
|
| plasmidfinder_results_raw | plasmidfinder_results_raw | n/a |
|
| plasmidfinder_hit_genome_fasta | plasmidfinder_hit_genome_fasta | n/a |
|
| plasmidfinder_results_tabular | plasmidfinder_results_tabular | n/a |
|
| plasmidfinder_result_json | plasmidfinder_result_json | n/a |
|
| plasmidfinder_hit_reference_fasta | plasmidfinder_hit_reference_fasta | n/a |
|
| bakta_annotation_tabular | bakta_annotation_tabular | n/a |
|
| bakta_assembly_fasta | bakta_assembly_fasta | n/a |
|
| bakta_summary_text | bakta_summary_text | n/a |
|
| bakta_annotation_plot | bakta_annotation_plot | n/a |
|
| bakta_hypothetical_faa | bakta_hypothetical_faa | n/a |
|
| bakta_hypothetical_tabular | bakta_hypothetical_tabular | n/a |
|
| bakta_annotation_embl | bakta_annotation_embl | n/a |
|
| bakta_annotation_gbff | bakta_annotation_gbff | n/a |
|
| bakta_aminoacid_sequence_faa | bakta_aminoacid_sequence_faa | n/a |
|
| bakta_nucleotide_sequence_fasta | bakta_nucleotide_sequence_fasta | n/a |
|
| bakta_annotation_gff3 | bakta_annotation_gff3 | n/a |
|
| tooldistillator_results_annotation_without_bakta | tooldistillator_results_annotation_without_bakta | n/a |
|
| bakta_annotation_json | bakta_annotation_json | n/a |
|
| tooldistillator_summarize_annotation_without_bakta | tooldistillator_summarize_annotation_without_bakta | n/a |
|
| tooldistillator_results_annotation_bakta | tooldistillator_results_annotation_bakta | n/a |
|
| tooldistillator_summarize_bakta | tooldistillator_summarize_bakta | n/a |
|
Version History
v1.2.0 (latest) Created 6th Dec 2025 at 03:02 by WorkflowHub Bot
Updated to v1.2.0
Frozen
v1.2.04429e30
v1.0 (earliest) Created 20th Jun 2024 at 03:02 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0
bb3655f
Creators and Submitter
Activity
Views: 11789 Downloads: 63333 Runs: 14
Created: 20th Jun 2024 at 03:01
AttributionsNone
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