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.

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
help Creators and Submitter
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Additional credit

VGP, Galaxy

Submitter
Activity

Views: 3197   Downloads: 415   Runs: 1

Created: 8th Feb 2024 at 03:01

Last updated: 29th May 2025 at 03:01

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