VGP-meryldb-creation/main
v0.1

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This workflow does not specify a "main" workflow file.

Workflow Type: Galaxy

Tests Passing

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.	File[]
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).	int?
Ploidy	Ploidy	Ploidy for model to use. Default=2	int?

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	File
GenomeScope summary	GenomeScope summary	n/a	File
GenomeScope model	GenomeScope model	n/a	File
GenomeScope transformed linear plot	GenomeScope transformed linear plot	n/a	File
GenomeScope linear plot	GenomeScope linear plot	n/a	File
GenomeScope log plot	GenomeScope log plot	n/a	File
GenomeScope transformed log plot	GenomeScope transformed log plot	n/a	File
GenomeScope model parameters	GenomeScope model parameters	n/a	File