VGP-meryldb-creation/main
Version 1

View on GitHub

Download RO Crate

Run on usegalaxy.eu

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

SEEK ID: https://workflowhub.eu/workflows/366?version=1

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
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

Frozen v0.1 7ccf2dd

Creators and Submitter

Creators

Not specified

Submitter

WorkflowHub Bot

License

Creative Commons Attribution 4.0

Activity

Views: 41

Created: 14th Jun 2022 at 03:01

Last used: 27th Jun 2022 at 14:17

VGP-meryldb-creation/main Version 1

VGP Workflow #1

Inputs

Outputs

Inputs

Steps

Outputs

Version History

v0.1 (earliest) Created 14th Jun 2022 at 03:01 by WorkflowHub Bot

Creators

Submitter

Related items

VGP-meryldb-creation/main
Version 1