VGP Workflow #1

This workflow collects the metrics on the properties of the genome under consideration by analyzing the k-mer frequencies. 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. It uses reads from two parental genomes to partition long reads from the offspring into haplotype-specific k-mer databases.

Inputs

• Collection of Hifi long reads [fastq] (Collection)
• Paternal short-read Illumina sequencing reads [fastq] (Collection)
• Maternal short-read Illumina sequencing reads [fastq] (Collection)
• k-mer length
• Ploidy

Outputs

• Meryl databases of k-mer counts

  • Child
  • Paternal haplotype
  • Maternal haplotype

• GenomeScope metrics for child and the two parental genomes (three GenomeScope profiles in total)

  • Linear plot
  • Log plot
  • Transformed linear plot
  • Transformed log plot
  • Summary
  • Model
  • Model parameteres

  

Changelog

[0.1.4] 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

[0.1.3] 2023-11-20

• Fix author in dockstore

[0.1.2] 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] - 2023-10-30

Added

• Clearer labels

Removed

• Interlacing step that was unneccessary
• Requirement for paired list inputs for the Illumina parental reads. A dataset collection list is sufficient now.
• Unnecessary workflow intputs

[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