kmer-profiling-hifi-VGP1/main
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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 | #main/Collection of Pacbio Data | A simple list collection containing PacBio data in either fastq or fasta format |
|
| K-mer length | #main/K-mer length | n/a |
|
| Ploidy | #main/Ploidy | Ploidy for the organism being assembled |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
| 4 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
| 5 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
| 6 | GenomeScope | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| GenomeScope Model Parameters | #main/GenomeScope Model Parameters | n/a |
|
| GenomeScope linear plot | #main/GenomeScope linear plot | n/a |
|
| GenomeScope log plot | #main/GenomeScope log plot | n/a |
|
| GenomeScope summary | #main/GenomeScope summary | n/a |
|
| GenomeScope transformed linear plot | #main/GenomeScope transformed linear plot | n/a |
|
| GenomeScope transformed log plot | #main/GenomeScope transformed log plot | n/a |
|
| Merged Meryl Database | #main/Merged Meryl Database | n/a |
|
Version History
v0.1.7 (latest) Created 7th Oct 2024 at 16:34 by WorkflowHub Bot
Updated to v0.1.7
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v0.1.707de7a2
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: 4452 Downloads: 823 Runs: 0
Created: 31st Oct 2023 at 03:01
Last updated: 8th Aug 2024 at 03:02
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Public web page: https://github.com/galaxyproject/iwc
