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

  • 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

image

Inputs

ID Name Description Type
Collection of Pacbio Data #main/Collection of Pacbio Data A simple list collection containing PacBio data in either fastq or fasta format
  • array containing
    • File
K-mer length #main/K-mer length n/a
  • int
Ploidy #main/Ploidy Ploidy for the organism being assembled
  • int

Steps

ID Name Description
3 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
4 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
5 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
6 GenomeScope toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2

Outputs

ID Name Description Type
GenomeScope Model Parameters #main/GenomeScope Model Parameters n/a
  • File
GenomeScope linear plot #main/GenomeScope linear plot n/a
  • File
GenomeScope log plot #main/GenomeScope log plot n/a
  • File
GenomeScope summary #main/GenomeScope summary n/a
  • File
GenomeScope transformed linear plot #main/GenomeScope transformed linear plot n/a
  • File
GenomeScope transformed log plot #main/GenomeScope transformed log plot n/a
  • File
Merged Meryl Database #main/Merged Meryl Database n/a
  • File

Version History

v0.1.5 (latest) Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.5


Frozen v0.1.5 015c711

v0.1.4 Created 17th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 bf98966

v0.1.3 Created 10th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.3


Frozen v0.1.3 b751646

v0.1.2 Created 8th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.2


Frozen v0.1.2 8a15e82

v0.1.1 (earliest) Created 31st Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.1


Frozen v0.1.1 270fb18
help Creators and Submitter
Creators
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Additional credit

VGP, Galaxy

Submitter
Activity

Views: 2254   Downloads: 364

Created: 31st Oct 2023 at 03:01

Last updated: 24th Nov 2023 at 03:02

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