VGP-meryldb-creation/main
Version 1

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.
  • 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

Version History

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

Updated to v0.1


Frozen v0.1 7ccf2dd
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Created: 14th Jun 2022 at 03:01

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