Analyses of shotgun metagenomics data with MetaPhlAn2 Version 1
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Run on usegalaxy.euThe 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
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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
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Views: 325
Created: 26th Oct 2023 at 20:34
Last updated: 14th Nov 2023 at 21:43
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Erasmus University Medical Centre
https://orcid.org/0000-0003-3803-468X
Post-doc at ErasmusMC, Galaxy Training Network (GTN) Lead
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
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/
