ERGA Profiling HiFi v2409 (WF1)
Version 2 (latest)

Version 2 (latest)

Version 1 (earliest)

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Run on Galaxy

Workflow Type: Galaxy

Stable

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.

SEEK ID: https://workflowhub.eu/workflows/603?version=2

Inputs

ID	Name	Description	Type
Ploidy	Ploidy	Default ploidy: 2	int?
Run Smudgeplot?	Run Smudgeplot?	n/a	boolean
Trimmed HiFi collection	Trimmed HiFi collection	n/a	File[]
kmer length	kmer length	Kmer length for calculating kmer spectra	int?

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	File
_anonymous_output_1	_anonymous_output_1	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
_anonymous_output_4	_anonymous_output_4	n/a	File
_anonymous_output_5	_anonymous_output_5	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
_anonymous_output_7	_anonymous_output_7	n/a	File
_anonymous_output_8	_anonymous_output_8	n/a	File
_anonymous_output_9	_anonymous_output_9	n/a	File
_anonymous_output_10	_anonymous_output_10	n/a	File
_anonymous_output_11	_anonymous_output_11	n/a	File
transition_parameter	transition_parameter	n/a	File
max_depth	max_depth	n/a	File
genome_size	genome_size	n/a	File