Workflows
What is a Workflow?Filters
Name: PhysioNet kNN Kfold Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5
Kfold to evaluate kNN accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0
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 |
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 |
Article-GADES
This repository represents generating and benchmarking the results of the GADES package for Distance Matrix Calculation
Installation
git lfs install
git clone https://github.com/lab-medvedeva/Article-GADES.git
cd Article-GADES
Put the Real datasets in the MEX format to the folder Datasets/Real
.
Running benchmark using Docker Deployment
docker run --gpus all \
-v $PWD/Datasets:/workspace/Article-GADES/Datasets
...
Name: PhysioNet CascadeCSVM Kfold Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5
Kfold to evaluate CascadeCSVM accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0
Name: PhysioNet RF Kfold Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5
Kfold to evaluate RandomForest accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0
Genome assembly workflow for nanopore reads, for TSI
Input:
- Nanopore reads (can be in format: fastq, fastq.gz, fastqsanger, or fastqsanger.gz)
Optional settings to specify when the workflow is run:
- [1] how many input files to split the original input into (to speed up the workflow). default = 0. example: set to 2000 to split a 60 GB read file into 2000 files of ~ 30 MB.
- [2] filtering: min average read quality score. default = 10
- [3] filtering: min read length. default = 200
- [4] ...
Process argo data with the Pangeo Ecosystem and visualise them with Ocean Data View (ODV)