1: Plant virus detection with kraken2 (PE) Version 1
Download RO-Crate
Run on GalaxyMetagenomic dataset taxonomic classification using kraken2
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Data_R1.fastq | Data_R1.fastq | n/a |
|
| Data_R2.fastq | Data_R2.fastq | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Kraken2: taxonomic prediction | provide different taxonomic prediction with several false positive. WARNING: consider changing the database toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy0 |
| 3 | Convert kraken file | just re-arrange the column of the tabular file so it can be ready for krona representation toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.2 |
| 4 | Krona pie chart | Improve kraken2 taxonomic result representation in a HTLM report toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Kraken_report | Kraken_report | n/a |
|
| Kraken_taxonomy_table | Kraken_taxonomy_table | n/a |
|
| Kraken_taxonomy_table_modified | Kraken_taxonomy_table_modified | n/a |
|
| Taxonomic_prediction_report | Taxonomic_prediction_report | n/a |
|
Version History
Version 1 (earliest) Created 4th Feb 2021 at 09:07 by johan Rollin
Added/updated 1 files
Open
master26feb9a
Creators and SubmitterViews: 4080 Downloads: 304 Runs: 0
Created: 4th Feb 2021 at 09:07
Last updated: 17th Jun 2021 at 10:10
AttributionsNone
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Teams: Integrated and Urban Plant Pathology Laboratory
Organizations: Liege university
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Web page: Not specified
Les recherches et enseignements développés par le Laboratoire de Phytopathologie Intégrée et Urbaine visent à améliorer la protection des plantes contre les maladies provoquées par les agents pathogènes et à développer de nouveaux modes de production agricole en milieu urbain. Le laboratoire contribue ainsi à répondre aux défis écologiques, environnementaux, climatiques et sociétaux de l’agriculture de demain.
Space: Independent Teams
Public web page: https://www.gembloux.ulg.ac.be/phytopathologie/
