Mitogenome-assembly-VGP0/main
v0.2.1 (latest)

v0.2.1 (latest)

v0.2

v0.1 (earliest)

Workflow Type: Galaxy

Generate 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.

SEEK ID: https://workflowhub.eu/workflows/738?version=3

Inputs

ID	Name	Description	Type
Assembly Name	Assembly Name	For Workflow report.	string
Collection of Pacbio Data	Collection of Pacbio Data	n/a	File[]
Email adress	Email adress	Required for NCBI database query	string
Species name (latin name)	Species name (latin name)	Latin name of the species. E.g. Homo Sapiens	string

Steps

ID	Name	Description
4	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
5	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
6	MitoHiFi	toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0
7	MitoHiFi	toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0
8	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	File
Assembly Name for report	Assembly Name for report	n/a	File
Mitogenome: Contigs Statistics	Mitogenome: Contigs Statistics	n/a	File
Mitogenome coverage: Image	Mitogenome coverage: Image	n/a	File
Mitogenome annotation: Image	Mitogenome annotation: Image	n/a	File
Mitogenome annotation: GenBank	Mitogenome annotation: GenBank	n/a	File
Compressed Mitogenome	Compressed Mitogenome	n/a	File

Version History

v0.2.1 (latest) Created 29th May 2025 at 03:01 by WorkflowHub Bot

Updated to v0.2.1

Frozen v0.2.1 87ca0c5

v0.2 Created 15th May 2025 at 03:01 by WorkflowHub Bot

Updated to v0.2

Frozen v0.2 ab4120d

v0.1 (earliest) Created 8th Feb 2024 at 03:01 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 97cce79

Creators and Submitter

Creators

Not specified

Additional credit

VGP, Galaxy

Submitter

WorkflowHub Bot

License

Creative Commons Attribution 4.0 International

Activity

Views: 3197 Downloads: 415 Runs: 1

Created: 8th Feb 2024 at 03:01

Last updated: 29th May 2025 at 03:01

Mitogenome-assembly-VGP0/main v0.2.1 (latest) v0.2.1 (latest) v0.2 v0.1 (earliest)