Workflow Type: Galaxy
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The workflow takes a trimmed HiFi reads collection, runs Meryl to create a K-mer database, Genomescope2 to estimate genome properties and Smudgeplot to estimate ploidy. The main results are K-mer database and genome profiling plots, tables, and values useful for downstream analysis. Default K-mer length and ploidy for Genomescope are 21 and 2, respectively.
Inputs
ID | Name | Description | Type |
---|---|---|---|
Ploidy | Ploidy | Default ploidy: 2 |
|
Run Smudgeplot? | Run Smudgeplot? | n/a |
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Trimmed HiFi collection | Trimmed HiFi collection | n/a |
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kmer length | kmer length | Kmer length for calculating kmer spectra |
|
Steps
ID | Name | Description |
---|---|---|
4 | Meryl-count | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
5 | Meryl-unionsum | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
6 | Meryl-histogram | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
7 | Smudgeplot | toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy3 |
8 | GenomeScope | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0 |
9 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 |
10 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
11 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 |
12 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
13 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
14 | Cut | Cut1 |
15 | Cut | Cut1 |
16 | Convert | Convert characters1 |
17 | Parse parameter value | param_value_from_file |
18 | Parse parameter value | param_value_from_file |
19 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 |
20 | Parse parameter value | param_value_from_file |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Merged Meryl DB | Merged Meryl DB | n/a |
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_anonymous_output_1 | _anonymous_output_1 | n/a |
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_anonymous_output_2 | _anonymous_output_2 | n/a |
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_anonymous_output_3 | _anonymous_output_3 | n/a |
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_anonymous_output_4 | _anonymous_output_4 | n/a |
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_anonymous_output_5 | _anonymous_output_5 | n/a |
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_anonymous_output_6 | _anonymous_output_6 | n/a |
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_anonymous_output_7 | _anonymous_output_7 | n/a |
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_anonymous_output_8 | _anonymous_output_8 | n/a |
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_anonymous_output_9 | _anonymous_output_9 | n/a |
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_anonymous_output_10 | _anonymous_output_10 | n/a |
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_anonymous_output_11 | _anonymous_output_11 | n/a |
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transition_parameter | transition_parameter | n/a |
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max_depth | max_depth | n/a |
|
genome_size | genome_size | n/a |
|
Version History
Version 2 (latest) Created 18th Sep 2024 at 14:27 by Diego De Panis
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Version 1 (earliest) Created 6th Oct 2023 at 14:25 by Diego De Panis
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ERGA
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Views: 2998 Downloads: 335 Runs: 29
Created: 6th Oct 2023 at 14:25
Last updated: 18th Sep 2024 at 14:28
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