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 |
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Input samplesheet file | Input samplesheet file | n/a |
|
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 |
|
Kraken2 combined report | Kraken2 combined report | n/a |
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Bracken combined report | Bracken combined report | n/a |
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Bracken krona text | Bracken krona text | n/a |
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Beta diversity summary text file | Beta diversity summary text file | n/a |
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Bracken species abundance combined results | Bracken species abundance combined results | n/a |
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Krona pie chart | Krona pie chart | n/a |
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Alpha diversity summary text file | Alpha diversity summary text file | n/a |
|
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
Creators
Submitter
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Created: 12th Nov 2024 at 06:57
Last updated: 9th Dec 2024 at 21:51
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