Assembly-decontamination-VGP9/main
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Workflow Type: Galaxy
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Tests
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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 | lower to uppercase | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
| 3 | soft-masking | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2 |
| 4 | hard-masking | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
| 5 | ID non-target contaminants | toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 |
| 6 | blast mitochondria DB | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2 |
| 7 | Cut | Cut1 |
| 8 | contaminant scaffolds | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 |
| 9 | parsing blast output | toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0 |
| 10 | Filter | Filter1 |
| 11 | remove > + lowercase | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
| 12 | to lowercase | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
| 13 | isolate scaffolds names | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
| 14 | concatenate scaffold lists | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1 |
| 15 | 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
v0.1 (earliest) Created 8th Nov 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1f74cf72
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Activity
Views: 4974 Downloads: 985 Runs: 0
Created: 8th Nov 2023 at 03:01
Last updated: 7th Oct 2024 at 16:34
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