Workflow Type: Galaxy
Open
Stable
The workflow takes a trimmed Illumina paired-end 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 ddatabase 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 | #main/Ploidy | Default ploidy: 2 |
|
Trimmed Illumina collection | #main/Trimmed Illumina collection | n/a |
|
kmer length | #main/kmer length | Kmer length for calculating kmer spectra |
|
Steps
ID | Name | Description |
---|---|---|
3 | Meryl-count | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
4 | Meryl-unionsum | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
5 | Meryl-histogram | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
6 | Smudgeplot | toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy3 |
7 | GenomeScope | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2 |
8 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 |
9 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
10 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 |
11 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
12 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
13 | Cut | Cut1 |
14 | Cut | Cut1 |
15 | Convert | Convert characters1 |
16 | Parse parameter value | param_value_from_file |
17 | Parse parameter value | param_value_from_file |
18 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 |
19 | Parse parameter value | param_value_from_file |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Merged Meryl DB | #main/Merged Meryl DB | n/a |
|
genome_size | #main/genome_size | n/a |
|
max_depth | #main/max_depth | n/a |
|
transition_parameter | #main/transition_parameter | n/a |
|
Version History
Version 1 (earliest) Created 8th Jan 2024 at 15:55 by Diego De Panis
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ERGA
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Created: 8th Jan 2024 at 15:55
Last updated: 8th Jan 2024 at 15:57
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