Workflow Type: Galaxy
Work-in-progress

The aim of this workflow is to handle the routine part of shotgun metagenomics data processing. The workflow is using the tools Kraken2 and Bracken for taxonomy classification and the KrakenTools to evaluate diversity metrics. This workflow was tested on Galaxy Australia. A How-to guide for the workflow can be found at: https://github.com/vmurigneu/kraken_howto_ga_workflows/blob/main/pages/taxonomy_kraken2_wf_guide.md

Inputs

ID Name Description Type
Input fastq collection Input fastq collection n/a
  • File[]
Input samplesheet file Input samplesheet file n/a
  • File

Steps

ID Name Description
2 Relabel identifiers __RELABEL_FROM_FILE__
3 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
4 Bracken toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0
5 Krakentools: Combine multiple Kraken reports toolshed.g2.bx.psu.edu/repos/iuc/krakentools_combine_kreports/krakentools_combine_kreports/1.2+galaxy2
6 Krakentools: Combine multiple Bracken reports toolshed.g2.bx.psu.edu/repos/iuc/krakentools_combine_kreports/krakentools_combine_kreports/1.2+galaxy2
7 Cut Extract column name and fraction_total_reads from Bracken report Cut1
8 Krakentools: Convert kraken report file toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1
9 Krakentools: Calculates alpha diversity (Shannon) toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1
10 Krakentools: Calculates alpha diversity (Simpson) toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1
11 Krakentools: Calculates alpha diversity (Fisher's index) toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1
12 Krakentools: calculates beta diversity (Bray-Curtis dissimilarity) toolshed.g2.bx.psu.edu/repos/iuc/krakentools_beta_diversity/krakentools_beta_diversity/1.2+galaxy1
13 Combine bracken species abundance toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
14 Krona pie chart toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
15 Extract sample identifers Extract sample identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
16 Concatenate alpha diversity results (Shannon) toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2
17 Concatenate alpha diversity results (Simpson) toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2
18 Select last line from fisher diversity Fisher results contains a header line we want to exclude "Fisher's alpha...loading" Show tail1
19 Sample identifers : regex find and replace Remove the suffixes of fastq files if required such as _S12_R1_001.fastq.gz toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
20 Alpha diversity : regex find and replace (Shannon) Remove the text such as "Shannon's diversity: " from the alpha diversity output line toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
21 Alpha diversity: regex find and replace (Simpson) Remove the text such as "Shannon's diversity: " from the alpha diversity output line toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
22 Concatenate alpha diversity results (Fisher's index) combine results for all samples toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2
23 Add header (sampleID) toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
24 Add header (Shannon) toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
25 Add header (Simpson) toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
26 Alpha diversity : regex find and replace (Fisher's index) Remove the text such as "Shannon's diversity: " from the alpha diversity output line toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
27 Paste sample identifiers and Shannon diversity Prepare alpha diversity summary file (paste sample identifiers and Simpson results) Paste1
28 Add header (Fisher's index) toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
29 Paste Simpson and Fisher diversity Prepare alpha diversity summary file (paste Simpson and Fisher results) Paste1
30 Alpha diversity summary file Prepare alpha diversity summary file Paste1

Outputs

ID Name Description Type
Input fastq collection renamed Input fastq collection renamed n/a
  • File
Kraken2 combined report Kraken2 combined report n/a
  • File
Bracken combined report Bracken combined report n/a
  • File
Bracken krona text Bracken krona text n/a
  • File
Beta diversity summary text file Beta diversity summary text file n/a
  • File
Bracken species abundance combined results Bracken species abundance combined results n/a
  • File
Krona pie chart Krona pie chart n/a
  • File
Alpha diversity summary text file Alpha diversity summary text file n/a
  • File

Version History

Version 2 (latest) Created 10th Dec 2024 at 23:58 by Valentine Murigneux

Correcting the DOI citation


Frozen Version-2 3c29fe8

Version 1 (earliest) Created 12th Nov 2024 at 06:57 by Valentine Murigneux

First stable release, after the following tool was fixed: toolshed.g2.bx.psu.edu/repos/iuc/krakentools_beta_diversity/krakentools_beta_diversity/1.2+galaxy2 cf https://github.com/galaxyproject/tools-iuc/pull/6553#event-15394514853


Frozen Version-1 3c29fe8
help Creators and Submitter
Citation
Murigneux, Q. C. I. F. B., & Thang, M. (2024). Taxonomy classification using Kraken2 and Bracken. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1199.1
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Created: 12th Nov 2024 at 06:57

Last updated: 9th Dec 2024 at 21:51

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