VGP-meryldb-creation-trio/main
Version 1

Workflow Type: Galaxy

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 in FASTQ format
  • Paternal short-read Illumina sequencing reads in FASTQ format
  • Maternal short-read Illumina sequencing reads in FASTQ format

Outputs

  • Meryl databases of k-mer counts
    • Child
    • Paternal haplotype
    • Maternal haplotype
  • GenomeScope metrics of child and parental genomes
    • Linear plot
    • Log plot
    • Transformed linear plot
    • Transformed log plot
    • Summary
    • Model
    • Model parameteres

Inputs

ID Name Description Type
Collection of Paired Reads - Maternal Collection of Paired Reads - Maternal Collection of Paired Illumina Data in fastq format for Parent 2.
  • File[]
Collection of Paired Reads - Paternal Collection of Paired Reads - Paternal Collection of Paired Illumina Data in fastq format for Parent 1.
  • 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?
Pacbio Hifi reads Pacbio Hifi reads n/a
  • File[]
Ploidy Ploidy Ploidy for model to use. Default=2
  • int?

Steps

ID Name Description
5 FASTQ interlacer toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0
6 FASTQ interlacer toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0
7 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
8 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
9 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
10 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
11 GenomeScope toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1
12 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
13 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
14 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
15 Genomescope on paternal haplotype toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1
16 Genomescope on maternal haplotype toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1

Outputs

ID Name Description Type
_anonymous_output_1 _anonymous_output_1 n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
Meryl pat.meryldb Meryl pat.meryldb n/a
  • File
Meryl mat.meryldb Meryl mat.meryldb n/a
  • File
Meryl read-db.meryldb Meryl read-db.meryldb n/a
  • File
GenomeScope summary (child) GenomeScope summary (child) n/a
  • File
GenomeScope transformed log plot (child) GenomeScope transformed log plot (child) n/a
  • File
GenomeScope transformed linear plot (child) GenomeScope transformed linear plot (child) n/a
  • File
GenomeScope linear plot (child) GenomeScope linear plot (child) n/a
  • File
GenomeScope model (child) GenomeScope model (child) n/a
  • File
GenomeScope log plot (child) GenomeScope log plot (child) n/a
  • File
GenomeScope log plot (paternal) GenomeScope log plot (paternal) n/a
  • File
GenomeScope transformed linear plot (paternal) GenomeScope transformed linear plot (paternal) n/a
  • File
GenomeScope linear plot (paternal) GenomeScope linear plot (paternal) n/a
  • File
GenomeScope transformed log plot (paternal) GenomeScope transformed log plot (paternal) n/a
  • File
GenomeScope transformed log plot (maternal) GenomeScope transformed log plot (maternal) n/a
  • File
GenomeScope transformed linear plot (maternal) GenomeScope transformed linear plot (maternal) n/a
  • File
GenomeScope linear plot (maternal) GenomeScope linear plot (maternal) n/a
  • File
GenomeScope log plot (maternal) GenomeScope log plot (maternal) 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 620df6d
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Created: 14th Jun 2022 at 03:01

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