kmer-profiling-hifi-VGP1/main
View on GitHub
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Frozen
Frozen
VGP Workflow #1
This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.
Inputs
- A collection of Hifi long reads in FASTQ format
- k-mer length
- Ploidy
Outputs
- Meryl Database of kmer counts
- GenomeScope
- Linear plot
- Log plot
- Transformed linear plot
- Transformed log plot
- Summary
- Model
- Model parameteres
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Collection of Pacbio Data | Collection of Pacbio Data | A simple list collection containing PacBio data in either fastq or fasta format |
|
| K-mer length | K-mer length | n/a |
|
| Ploidy | Ploidy | Ploidy for the organism being assembled |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 4 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7 |
| 5 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7 |
| 6 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7 |
| 7 | GenomeScope | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Merged Meryl Database | Merged Meryl Database | n/a |
|
| GenomeScope transformed linear plot | GenomeScope transformed linear plot | n/a |
|
| GenomeScope transformed log plot | GenomeScope transformed log plot | n/a |
|
| GenomeScope summary | GenomeScope summary | n/a |
|
| GenomeScope Model Parameters | GenomeScope Model Parameters | n/a |
|
| GenomeScope log plot | GenomeScope log plot | n/a |
|
| GenomeScope linear plot | GenomeScope linear plot | n/a |
|
Version History
v0.1.8 (latest) Created 12th Dec 2024 at 03:02 by WorkflowHub Bot
Updated to v0.1.8
Frozen
v0.1.826f3aa0
v0.1.1 (earliest) Created 31st Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1.1
Frozen
v0.1.1
270fb18
Creators and Submitter
Tool
Activity
Views: 5195 Downloads: 985 Runs: 1
Created: 31st Oct 2023 at 03:01
Last updated: 12th Dec 2024 at 03:02
TagsThis item has not yet been tagged.
AttributionsNone
Related items
Advanced Teams list for this Workflow with search and filtering
IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
