Mitogenome-assembly-VGP0/main
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Run on GalaxyGenerate mitochondrial assembly based on PacBio HiFi reads. Part of the VGP suite, it can be run at any time independently of the other workflows. This workflow uses MitoHiFi and a mitochondrial reference to assemble the mitochondrial genome from PacBio reads. You do not need to provide the reference yourself, only the Latin name of the species.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Assembly Name | Assembly Name | For Workflow report. |
|
| Collection of Pacbio Data | Collection of Pacbio Data | n/a |
|
| Email adress | Email adress | Required for NCBI database query |
|
| Genetic Code | Genetic Code | Organism genetic code following NCBI table (for mitogenome annotation) |
|
| Species name (latin name) | Species name (latin name) | Latin name of the species. E.g. Homo Sapiens |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 6 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 7 | MitoHiFi | toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0 |
| 8 | MitoHiFi | toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0 |
| 9 | Compress file(s) | toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Species Name for report | Species Name for report | n/a |
|
| Assembly Name for report | Assembly Name for report | n/a |
|
| Mitogenome coverage: Image | Mitogenome coverage: Image | n/a |
|
| Mitogenome annotation: Image | Mitogenome annotation: Image | n/a |
|
| Mitogenome annotation: GenBank | Mitogenome annotation: GenBank | n/a |
|
| Mitogenome: Contigs Statistics | Mitogenome: Contigs Statistics | n/a |
|
| Compressed Mitogenome | Compressed Mitogenome | n/a |
|
Version History
v0.2.2 (latest) Created 29th Aug 2025 at 03:01 by WorkflowHub Bot
Updated to v0.2.2
Frozen
v0.2.2ddcca42
v0.1 (earliest) Created 8th Feb 2024 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
97cce79
Creators and Submitter
Views: 5068 Downloads: 3531 Runs: 4
Created: 8th Feb 2024 at 03:01
Last updated: 29th Aug 2025 at 03:01
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