Assembly-decontamination-VGP9/main
View on GitHub
Download RO-Crate
Run on GalaxyDecontamination (foreign contaminants and mitochondrial sequences) of a genome assembly after the final scaffolding step. Uses NCBI FCS GX to identify foreign contaminants and Blast to identify mitochondrial sequences. Part of the VGP Suite.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Assembly Name | Assembly Name | For Workflow report |
|
| Database for NCBI FCS GX | Database for NCBI FCS GX | n/a |
|
| Haplotype | Haplotype | For Workflow report |
|
| Maximum length of sequence to consider for mitochondrial scaffolds | Maximum length of sequence to consider for mitochondrial scaffolds | If set to 0, use all sequences. Use this parameter if you have large contigs that cause Blast to fail. |
|
| Scaffolded assembly (fasta) | Scaffolded assembly (fasta) | n/a |
|
| Species Binomial Name | Species Binomial Name | NCBI Species Name. E.g. Homo Sapiens |
|
| Taxonomic Identifier | Taxonomic Identifier | NCBI taxon ID. E.g. 9606 for Homo Sapiens. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | NCBI FCS Adaptor | toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0 |
| 8 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 9 | Modify action report | n/a |
| 10 | NCBI FCS GX | toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.5+galaxy2 |
| 11 | soft-masking | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.16.0+galaxy0 |
| 12 | Filter sequences by length | toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2 |
| 13 | NCBI FCS GX | toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.5+galaxy2 |
| 14 | hard-masking | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2 |
| 15 | NCBI FCS GX | toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.5+galaxy2 |
| 16 | blast mitochondria DB | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.16.0+galaxy0 |
| 17 | parsing blast output | toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0 |
| 18 | removing scaffolds | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Adaptor Report | Adaptor Report | n/a |
|
| Assembly Info | Assembly Info | n/a |
|
| Masking Action Report | Masking Action Report | n/a |
|
| Taxonomy Report | Taxonomy Report | n/a |
|
| Contaminants report | Contaminants report | n/a |
|
| Contaminants sequences | Contaminants sequences | n/a |
|
| Mitochondrial Scaffolds | Mitochondrial Scaffolds | 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 SubmitterViews: 11917 Downloads: 17081 Runs: 10
Created: 8th Nov 2023 at 03:01
Last updated: 8th Oct 2025 at 03:01
TagsThis item has not yet been tagged.
AttributionsNone
Related items
Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
Teams: Vertebrate Genomes Pipelines in Galaxy
Organizations: Galaxy
https://orcid.org/0000-0001-6421-3484
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.
You can contribute too!
Space: Galaxy
Public web page: https://iwc.galaxyproject.org/
