kmer-profiling-hifi-VGP1/main
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Evaluation of Pacbio Hifi Reads and genome profiling. Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Assembly Name | Assembly Name | For Workflow report. |
|
| Collection of Pacbio Data | Collection of Pacbio Data | A simple list collection containing PacBio data in either fastq or fasta format |
|
| K-mer length | K-mer length | n/a |
|
| Ploidy | Ploidy | Ploidy for the organism being assembled |
|
| Species Name | Species Name | For Workflow report. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 6 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 7 | Mash evaluation | n/a |
| 8 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7 |
| 9 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 10 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7 |
| 11 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7 |
| 12 | GenomeScope | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0 |
| 13 | Parse kcov | n/a |
| 14 | Image Montage | toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy0 |
| 15 | Parse Estimated Genome Size | n/a |
| 16 | Homozygous Read Coverage | param_value_from_file |
| 17 | Estimated Genome Size | param_value_from_file |
| 18 | Parse parameter value | param_value_from_file |
| 19 | Rdeval Stats | toolshed.g2.bx.psu.edu/repos/richard-burhans/rdeval/rdeval/0.0.7+galaxy5 |
| 20 | rdeval report | toolshed.g2.bx.psu.edu/repos/richard-burhans/rdeval/rdeval_report/0.0.7+galaxy5 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Species for report | Species for report | n/a |
|
| Assembly for report | Assembly for report | n/a |
|
| HeatMap | HeatMap | n/a |
|
| Data for Interactive HeatMap | Data for Interactive HeatMap | n/a |
|
| K-mer length for report | K-mer length for report | n/a |
|
| Merged Meryl Database | Merged Meryl Database | n/a |
|
| GenomeScope Model Parameters | GenomeScope Model Parameters | n/a |
|
| GenomeScope log plot | GenomeScope log plot | n/a |
|
| GenomeScope linear plot | GenomeScope linear plot | n/a |
|
| GenomeScope transformed linear plot | GenomeScope transformed linear plot | n/a |
|
| GenomeScope transformed log plot | GenomeScope transformed log plot | n/a |
|
| GenomeScope summary | GenomeScope summary | n/a |
|
| Montage Genomescope | Montage Genomescope | n/a |
|
| Estimated Genome Size File | Estimated Genome Size File | n/a |
|
| Homozygous Read Coverage | Homozygous Read Coverage | n/a |
|
| Est_size_param | Est_size_param | n/a |
|
| Reads Statistics | Reads Statistics | n/a |
|
| Rdeval report | Rdeval report | n/a |
|
Version History
v0.1.1 (earliest) Created 31st Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1.1
Frozen
v0.1.1270fb18
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Activity
Views: 11115 Downloads: 8984 Runs: 3
Created: 31st Oct 2023 at 03:01
Last updated: 8th Oct 2025 at 03:02
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