This workflow does not specify a "main" workflow file.
Workflow Type: Galaxy
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
- Collection of Hifi long reads in FASTQ format
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 | Collection of Pacbio Data in fastq format. |
|
K-mer length | K-mer length | K-mer length used to calculate k-mer spectra. For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G). |
|
Ploidy | Ploidy | Ploidy for model to use. Default=2 |
|
Steps
ID | Name | Description |
---|---|---|
3 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy5 |
4 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy5 |
5 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy5 |
6 | GenomeScope | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Merged Meryl Database | Merged Meryl Database | n/a |
|
GenomeScope summary | GenomeScope summary | n/a |
|
GenomeScope model | GenomeScope model | n/a |
|
GenomeScope transformed linear plot | GenomeScope transformed linear plot | n/a |
|
GenomeScope linear plot | GenomeScope linear plot | n/a |
|
GenomeScope log plot | GenomeScope log plot | n/a |
|
GenomeScope transformed log plot | GenomeScope transformed log plot | n/a |
|
GenomeScope model parameters | GenomeScope model parameters | n/a |
|
Version History
v0.1 (earliest) Created 14th Jun 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
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v0.1
7ccf2dd
Creators and Submitter
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Views: 2885 Downloads: 202 Runs: 0
Created: 14th Jun 2022 at 03:01
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