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
tool | version | license |
---|---|---|
SeqSero2 | 1.2.1 | GNU GPL v2.0 |
BBTools | 39.01 | MIT License |
SRST2 | 0.2.0 | BSD License |
hamronize | 1.0.3 | GNU LGPL v3.0 |
SPAdes | v3.15.5 | GNU GPL v2.0 |
SKESA | 3.0.0 | Public Domain |
pilon | 1.1.0 | GNU GPL v2.0 |
shovill | 1.0.4 | GPL-3.0 license |
sistr | 1.1.1 | Apache-2.0 license |
MOB-Recon | 3.0.3 | Apache-2.0 license |
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: 4682 Downloads: 328 Runs: 1
Created: 24th Nov 2022 at 13:42
Last updated: 9th Sep 2024 at 09:23
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