Assembly-decontamination-VGP9/main
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Decontamination (foreign contaminants and mitochondrial sequences) of a genome assembly after the final scaffolding step. Uses Kraken2 to identify foreign contaminants and Blast to identify mitochondrial sequences. Part of the VGP Suite.
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/2.16.0+galaxy0 |
| 3 | hard-masking | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0 |
| 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/2.16.0+galaxy0 |
| 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/9.5+galaxy0 |
| 11 | removing scaffolds | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+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
Creators and Submitter
Activity
Views: 8211 Downloads: 1973 Runs: 5
Created: 8th Nov 2023 at 03:01
Last updated: 15th May 2025 at 03:03
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