ERGA Profiling Illumina v2311 (WF1)
Version 1

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.

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

Version History

Version 1 (earliest) Created 8th Jan 2024 at 15:55 by Diego De Panis

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Created: 8th Jan 2024 at 15:55

Last updated: 8th Jan 2024 at 15:57

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