mrsa AMR gene detection
1.0

Workflow Type: Galaxy

Identification of AMR genes in an assembled bacterial genome

Associated Tutorial

This workflows is part of the tutorial Identification of AMR genes in an assembled bacterial genome, available in the GTN

Features

Thanks to...

Workflow Author(s): Bazante Sanders, Bérénice Batut

Tutorial Author(s): Bazante Sanders, Bérénice Batut

Tutorial Contributor(s): Helena Rasche, Bazante Sanders, Saskia Hiltemann, Miaomiao Zhou, Deepti Varshney, pimarin, Bérénice Batut, Anthony Bretaudeau, Björn Grüning

Funder(s): Avans Hogeschool, ABRomics, ELIXIR Europe

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
contigs contigs n/a
  • File
forward_reads forward_reads n/a
  • File
reverse_reads reverse_reads n/a
  • File

Steps

ID Name Description
3 staramr toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1
4 Bakta toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0
5 Bowtie2 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0
6 Select Grep1
7 Table to GFF3 toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2
8 JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1

Outputs

ID Name Description Type
stararm_detailed_summary stararm_detailed_summary n/a
  • File
bakta_annotation_summary bakta_annotation_summary n/a
  • File
bowtie_mapping_stats bowtie_mapping_stats n/a
  • File
jbrowse_output jbrowse_output n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:55 by GTN Bot

Added/updated 4 files


Open master 4caca19
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Created: 2nd Jun 2025 at 10:55

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