The aim of this workflow is to handle the routine part of shotgun metagenomics data processing on Galaxy Australia.
The workflow is using the tools MetaPhlAn2 for taxonomy classification and HUMAnN2 for functional profiling of the metagenomes. The workflow is based on the Galaxy Training tutorial 'Analyses of metagenomics data - The global picture' (Saskia Hiltemann, Bérénice Batut) https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html#shotgun-metagenomics-data.
The how-to guide is available here: https://vmurigneu.github.io/shotgun_howto_ga_workflows/
Steps
ID | Name | Description |
---|---|---|
1 | MetaPhIAn2 | toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.1 |
2 | Extract relative abundance from MetaPhlAn output | Cut1 |
3 | Extract number of reads table from MetaPhlAn output for diversity stats | n/a |
4 | Format MetaPhlAn2 | toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0 |
5 | Merge | toolshed.g2.bx.psu.edu/repos/iuc/merge_metaphlan_tables/merge_metaphlan_tables/2.6.0.0 |
6 | HUMAnN2 | toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.3 |
7 | Krona pie chart | toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 |
8 | Rename Metaphlan output with sampleID | n/a |
9 | Join HUMAnN2 tables from a collection | n/a |
10 | Regroup gene families abundance | toolshed.g2.bx.psu.edu/repos/iuc/humann2_regroup_table/humann2_regroup_table/0.11.1.1 |
11 | Join HUMAnN2 tables from a collection | n/a |
12 | Renormalize gene families abundance | toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.11.1.1 |
13 | Renormalizse Pathways abundance | toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.11.1.1 |
14 | Renormalize regrouped gene families abundance | toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.11.1.1 |
15 | Join HUMAnN2 tables from a collection | n/a |
16 | Join HUMAnN2 tables from a collection | n/a |
17 | Join HUMAnN2 tables from a collection | n/a |
Version History
Version 1 (earliest) Created 26th Oct 2023 at 20:34 by Valentine Murigneux
Initial commit
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Creators
Additional credit
The workflow is based on the Galaxy Training tutorial Analyses of metagenomics data. Thank you to the Galaxy Australia team, Igor Makunin and Mike Thang for help with the workflow
Submitter
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Created: 26th Oct 2023 at 20:34
Last updated: 14th Nov 2023 at 21:43

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