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.

SEEK ID: https://workflowhub.eu/workflows/1050?version=9

Inputs

ID Name Description Type
Input sequence fasta #main/Input sequence fasta Can be any fasta file.
  • File
Select a AMRFinderPlus database #main/Select a AMRFinderPlus database Select a database to annotate AMR genes with Bakta.
  • string
Select a bacterial genome annotation database #main/Select a bacterial genome annotation database Select a database to predict CDS and small proteins (sORF) with Bakta.
  • string
Select a plasmid detection database #main/Select a plasmid detection database Select a database to identify plasmids with PlasmidFinder.
  • string

Steps

ID Name Description
4 genomic_annotation_insertionelement_isescan genomic_annotation_insertionelement_isescan toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1
5 genomic_annotation_integron genomic_annotation_integron toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0
6 genomic_annotation_plasmid_plasmidfinder genomic_annotation_plasmid_plasmidfinder toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1
7 Bakta toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0
8 ToolDistillator ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy1
9 ToolDistillator summarize ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1

Outputs

ID Name Description Type
bakta_aminoacid_sequence_faa #main/bakta_aminoacid_sequence_faa n/a
  • File
bakta_annotation_embl #main/bakta_annotation_embl n/a
  • File
bakta_annotation_gbff #main/bakta_annotation_gbff n/a
  • File
bakta_annotation_gff3 #main/bakta_annotation_gff3 n/a
  • File
bakta_annotation_json #main/bakta_annotation_json n/a
  • File
bakta_annotation_plot #main/bakta_annotation_plot n/a
  • File
bakta_annotation_tabular #main/bakta_annotation_tabular n/a
  • File
bakta_assembly_fasta #main/bakta_assembly_fasta n/a
  • File
bakta_hypothetical_faa #main/bakta_hypothetical_faa n/a
  • File
bakta_hypothetical_tabular #main/bakta_hypothetical_tabular n/a
  • File
bakta_nucleotide_sequence_fasta #main/bakta_nucleotide_sequence_fasta n/a
  • File
bakta_summary_text #main/bakta_summary_text n/a
  • File
integronfinder2_logfile_text #main/integronfinder2_logfile_text n/a
  • File
integronfinder2_results_tabular #main/integronfinder2_results_tabular n/a
  • File
integronfinder2_summary #main/integronfinder2_summary n/a
  • File
isescan_annotation_gff3 #main/isescan_annotation_gff3 n/a
  • File
isescan_is_fasta #main/isescan_is_fasta n/a
  • File
isescan_logfile_text #main/isescan_logfile_text n/a
  • File
isescan_orf_faa #main/isescan_orf_faa n/a
  • File
isescan_orf_fasta #main/isescan_orf_fasta n/a
  • File
isescan_results_tabular #main/isescan_results_tabular n/a
  • File
isescan_summary_tabular #main/isescan_summary_tabular n/a
  • File
plasmidfinder_hit_genome_fasta #main/plasmidfinder_hit_genome_fasta n/a
  • File
plasmidfinder_hit_reference_fasta #main/plasmidfinder_hit_reference_fasta n/a
  • File
plasmidfinder_result_json #main/plasmidfinder_result_json n/a
  • File
plasmidfinder_results_raw #main/plasmidfinder_results_raw n/a
  • File
plasmidfinder_results_tabular #main/plasmidfinder_results_tabular n/a
  • File
tooldistillator_results #main/tooldistillator_results n/a
  • File
tooldistillator_summarize #main/tooldistillator_summarize n/a
  • File

Version History

v1.1.7 (latest) Created 26th Oct 2024 at 03:02 by WorkflowHub Bot

Updated to v1.1.7


Frozen v1.1.7 941b952

v1.1.6 Created 12th Oct 2024 at 03:02 by WorkflowHub Bot

Updated to v1.1.6


Frozen v1.1.6 a7737bf

v1.1.5 Created 7th Oct 2024 at 16:31 by WorkflowHub Bot

Updated to v1.1.5


Frozen v1.1.5 1efe8e2

v1.1.4 Created 7th Oct 2024 at 16:31 by WorkflowHub Bot

Updated to v1.1.4


Frozen v1.1.4 de8a9cc

v1.1.3 Created 7th Oct 2024 at 16:31 by WorkflowHub Bot

Updated to v1.1.3


Frozen v1.1.3 6677904

v1.1.2 Created 20th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v1.1.2


Frozen v1.1.2 082a807

v1.1.1 Created 11th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v1.1.1


Frozen v1.1.1 87aa4a0

v1.1 Created 25th Jun 2024 at 03:02 by WorkflowHub Bot

Updated to v1.1


Frozen v1.1 012a760

v1.0 (earliest) Created 20th Jun 2024 at 03:02 by WorkflowHub Bot

Updated to v1.0


Frozen v1.0 bb3655f
help Creators and Submitter
Creators
  • ABRomics
  • Pierre Marin
  • Clea Siguret
Additional credit

abromics-consortium

Submitter
Tools
ISEScan
Integron Finder
PlasmidFinder
ToolDistillator
License
GNU General Public License v3.0 or later
Activity

Views: 2074   Downloads: 641   Runs: 1

Created: 20th Jun 2024 at 03:01

help Attributions

None

Total size: 62.5 KB
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