Workflow 3: CFIA
Version 1

Workflow Type: Galaxy
Work-in-progress

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

Steps

ID Name Description
1 SeqSero - raw allele toolshed.g2.bx.psu.edu/repos/ddollee/seqsero2/seqsero2/1.2.1+galaxy0
2 SRST2 toolshed.g2.bx.psu.edu/repos/nml/srst2/srst2/0.3.7
3 BBTools: BBduk toolshed.g2.bx.psu.edu/repos/iuc/bbtools_bbduk/bbtools_bbduk/39.01+galaxy0
4 Map with KMA toolshed.g2.bx.psu.edu/repos/iuc/kma/kma_map/1.2.21+galaxy1
5 SeqSero2 - raw k-mer toolshed.g2.bx.psu.edu/repos/ddollee/seqsero2/seqsero2/1.2.1+galaxy0
6 hamronize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1
7 BBTools: Tadpole toolshed.g2.bx.psu.edu/repos/iuc/bbtools_tadpole/bbtools_tadpole/39.01+galaxy0
8 SPAdes + pilon toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1
9 SKESA + pilon toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1
10 SeqSero - assemblies toolshed.g2.bx.psu.edu/repos/ddollee/seqsero2/seqsero2/1.2.1+galaxy0
11 Resistance Gene Identifier (RGI) toolshed.g2.bx.psu.edu/repos/card/rgi/rgi/5.2.1
12 sistr_cmd toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1+galaxy1
13 MOB-Recon toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/3.0.3+galaxy0
14 Resistance Gene Identifier (RGI) toolshed.g2.bx.psu.edu/repos/card/rgi/rgi/5.2.1
15 hamronize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1
16 hamronize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1
17 hamronize: summarize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2

Version History

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

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Views: 1856

Created: 24th Nov 2022 at 13:42

Last updated: 30th Oct 2023 at 16:50

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