ERGA Profiling Illumina v2311 (WF1)
Version 1

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Run on usegalaxy.eu

Workflow Type: Galaxy

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.

SEEK ID: https://workflowhub.eu/workflows/698?version=1

Inputs

ID	Name	Description	Type
Ploidy	#main/Ploidy	Default ploidy: 2	int
Trimmed Illumina collection	#main/Trimmed Illumina collection	n/a	array containing File
kmer length	#main/kmer length	Kmer length for calculating kmer spectra	int

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	File
genome_size	#main/genome_size	n/a	File
max_depth	#main/max_depth	n/a	File
transition_parameter	#main/transition_parameter	n/a	File