Taxonomy classification using Kraken2 and Bracken
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Run on GalaxyThe 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 |
|
| 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 |
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| 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-23c29fe8
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 and Submitter
Views: 643 Downloads: 108 Runs: 10
Created: 12th Nov 2024 at 06:57
Last updated: 9th Dec 2024 at 21:51
AttributionsNone
Related items
Teams: Galaxy Australia, QCIF Bioinformatics
Organizations: QCIF
https://orcid.org/0000-0002-1480-3563
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia, National Computational Infrastructure (NCI) WorkflowHub team
Web page: https://www.biocommons.org.au/
Working closely with researchers, the QCIF Bioinformatics team apply data management, processing, integration, analysis and visualisation techniques to maximise the potential value of biological and clinical data sets. QCIF Bioinformatics is a partner in the Australian BioCommons.
Space: Australian BioCommons
Public web page: https://www.qcif.edu.au/
