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

Changelog

[0.1.7] 2024-08-05

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2 was updated to toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0

[0.1.6] 2024-07-12

• Add workflow report

[0.1.5] 2023-11-20

• Fix author in dockstore

[0.1.4] 2023-11-15

Added

• more descriptive labels for inputs

[0.1.3] 2023-11-09

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2

[0.1.2] - 2023-11-07

Changed

• Added tag filtering for inputs

[0.1.1] - 2023-10-30

Changed

• Names of the workflow and viles for consistency with other VGP workflows
• Labels and tags for user readability

[0.1] - 2021-08-26

Added

• First version of the workflow.

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
• toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0