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. | n/a |
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). | n/a |
Ploidy | Ploidy | Ploidy for model to use. Default=2 | n/a |
input | input | runtime parameter for tool GenomeScope | n/a |
Steps
ID | Name | Description |
---|---|---|
0 | Collection of Pacbio Data | Collection of Pacbio Data in fastq format. |
1 | 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). |
2 | Ploidy | Ploidy for model to use. Default=2 |
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 |
---|---|---|---|
read_db | read_db | n/a | |
read_db | read_db | n/a | |
read_db_hist | read_db_hist | n/a | |
linear_plot | linear_plot | n/a | |
log_plot | log_plot | n/a | |
transformed_linear_plot | transformed_linear_plot | n/a | |
transformed_log_plot | transformed_log_plot | n/a | |
model | model | n/a | |
summary | summary | n/a | |
model_params | model_params | 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

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Created: 14th Jun 2022 at 03:01
Last used: 27th Jun 2022 at 14:17

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