Taxonomy classification using Kraken2 and Bracken Version 1
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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
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 |
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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 1 (earliest) Created 12th Nov 2024 at 06:57 by Valentine Murigneux
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Views: 152 Downloads: 44 Runs: 5
Created: 12th Nov 2024 at 06:57
Last updated: 12th Nov 2024 at 07:10
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https://orcid.org/0000-0002-1235-9462
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.
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