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.

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

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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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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