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. n/a
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). n/a
Ploidy Ploidy Ploidy for model to use. Default=2 n/a
input input runtime parameter for tool GenomeScope n/a

Steps

ID Name Description
0 Collection of Pacbio Data Collection of Pacbio Data in fastq format.
1 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).
2 Ploidy Ploidy for model to use. Default=2
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
read_db read_db n/a
read_db read_db n/a
read_db_hist read_db_hist n/a
linear_plot linear_plot n/a
log_plot log_plot n/a
transformed_linear_plot transformed_linear_plot n/a
transformed_log_plot transformed_log_plot n/a
model model n/a
summary summary n/a
model_params model_params n/a

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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Views: 265

Created: 14th Jun 2022 at 03:01

Last used: 6th Dec 2022 at 04:12

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