Workflows
What is a Workflow?Filters
Query
Created At
Updated At
Tool
shovill2
ABRicate1
BBMap1
BWA1
hAMRonization1
MOB-suite1
pilon1
SeqSero21
SISTR1
SPAdes1
staramr1
More...
Workflow type
Galaxy5
Tag
AMR2
AMR-detection2
antimicrobial resistance2
Bioinformatics2
10.3390/microorganisms100202921
benchamrking1
Space
Independent Teams5
Operation annotations
Antimicrobial resistance prediction1
Maturity
Work-in-progress3
5
Workflows visible to you, out of a total of 5
Work-in-progress
This is an aggregation of the work done in Seq4AMR consisting of the following workflows:
- WF1: AbritAMR / AMRFinderPlus
- WF2: Sciensano (not currently included)
- WF3: SRST2
- WF4: StarAMR
Installation
- You will need to:
- run the [RGI Database ...
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 |
| ... |
| database | database version |
|---|---|
| ResFinder | 2022-07-19 |
| CARD | 2023-12-03 |
Work-in-progress
Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr.
Doi: 10.3390/microorganisms10020292
| tool | version | license |
|---|---|---|
| staramr | 0.8.0 | Apache-2.0 license |
