Workflow 3: AMR - SeqSero2/SISTR
Version 0.1

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/iuc/seqsero2/seqsero2/1.2.1+galaxy0
2 Unzip collection __UNZIP_COLLECTION__
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 SeqSero - raw k-mer toolshed.g2.bx.psu.edu/repos/iuc/seqsero2/seqsero2/1.2.1+galaxy0
6 SRST2 toolshed.g2.bx.psu.edu/repos/iuc/srst2/srst2/0.2.0+galaxy1
7 BBTools: Tadpole toolshed.g2.bx.psu.edu/repos/iuc/bbtools_tadpole/bbtools_tadpole/39.01+galaxy0
8 hamronize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1
9 SPAdes + pilon toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1
10 SKESA + pilon toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1
11 hamronize: summarize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2
12 SeqSero2 toolshed.g2.bx.psu.edu/repos/iuc/seqsero2/seqsero2/1.2.1+galaxy0
13 sistr_cmd toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1+galaxy1
14 MOB-Recon toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/3.0.3+galaxy0

Version History

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

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Views: 2868   Downloads: 199

Created: 24th Nov 2022 at 13:42

Last updated: 7th May 2024 at 10:45

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