Workflow 3: AMR - SeqSero2/SISTR Version 0.1
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Run on GalaxyWith 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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Creators and SubmitterViews: 3619 Downloads: 254 Runs: 0
Created: 24th Nov 2022 at 13:42
Last updated: 7th May 2024 at 10:45
AttributionsNone
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Organizations: Erasmus University Medical Centre
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Public web page: https://erasmusmc-bioinformatics.github.io/benchAMRking/
