Workflow Type: Galaxy
Open
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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Created: 24th Nov 2022 at 13:42
Last updated: 30th Oct 2023 at 16:50

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