Workflow 3: CFIA
Version 1

Workflow Type: Galaxy

With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.

This pipeline is based on the work of the National Food Agency of Canada.
Doi: 10.3389/fmicb.2020.00549


ID Name Description
1 SeqSero - raw allele
3 BBTools: BBduk
4 Map with KMA
5 SeqSero2 - raw k-mer
6 hamronize
7 BBTools: Tadpole
8 SPAdes + pilon
9 SKESA + pilon
10 SeqSero - assemblies
11 Resistance Gene Identifier (RGI)
12 sistr_cmd
13 MOB-Recon
14 Resistance Gene Identifier (RGI)
15 hamronize
16 hamronize
17 hamronize: summarize

Version History

Version 0.1 (earliest) Created 24th Nov 2022 at 13:42 by Dennis Dollée

Update workflow

Open master c46138e
help Creators and Submitter
Not specified

Views: 1189

Created: 24th Nov 2022 at 13:42

Last updated: 30th Oct 2023 at 16:50

help Attributions


Total size: 312 MB

Brought to you by:

Powered by
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH