Assembly-decontamination-VGP9 1.0
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This workflows is part of the tutorial Decontamination of a genome assembly, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Nadolina Brajuka
Tutorial Author(s): Delphine Lariviere
Tutorial Contributor(s): Saskia Hiltemann, Deepti Varshney, Delphine Lariviere, Björn Grüning, Bérénice Batut
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Database for Kraken2 | Database for Kraken2 | Select the database to query to identify non-target contaminants. |
|
| Scaffolded assembly (fasta) | Scaffolded assembly (fasta) | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | soft-masking | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2 |
| 3 | hard-masking | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
| 4 | ID non-target contaminants | toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 |
| 5 | blast mitochondria DB | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2 |
| 6 | Cut | Cut1 |
| 7 | parsing blast output | toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0 |
| 8 | Filter | Filter1 |
| 9 | Cut | Cut1 |
| 10 | concatenate scaffold lists | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1 |
| 11 | removing scaffolds | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Kraken2 classification scores | Kraken2 classification scores | n/a |
|
| mito_scaff_names | mito_scaff_names | n/a |
|
| contaminants_table | contaminants_table | n/a |
|
| full contaminant + mito scaffold list | full contaminant + mito scaffold list | n/a |
|
| final decontaminated assembly | final decontaminated assembly | n/a |
|
Version History
master
Creators and Submitter
Views: 230 Downloads: 27 Runs: 0
Created: 2nd Jun 2025 at 11:00
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