mrsa AMR gene detection

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Workflow Type: Galaxy

Identification of AMR genes in an assembled bacterial genome

Associated Tutorial

This workflows is part of the tutorial mrsa AMR gene detection, available in the GTN

Features

Thanks to...

Tutorial Author(s): Bazante Sanders, Bérénice Batut

Tutorial Contributor(s): Helena Rasche, Bazante Sanders, Saskia Hiltemann, Miaomiao Zhou

Workflow Author(s): Bazante Sanders, Bérénice Batut

Funder(s): Avans Hogeschool, ABRomics

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1168?version=1

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 (latest) Created 16th Jul 2024 at 14:04 by Helena Rasche

Added/updated 4 files


Open master edb880e

4.0 (earliest) Created 25th Jun 2024 at 11:05 by Helena Rasche

Added/updated 4 files


Frozen 4.0 84ada6d
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
staramr
Bakta
Bowtie 2
tbl2gff3
JBrowse
License
MIT License
Activity

Views: 573   Downloads: 177

Created: 25th Jun 2024 at 11:05

Last updated: 25th Jun 2024 at 11:05

help Attributions

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Total size: 85.3 KB
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