Analyses of shotgun metagenomics data with MetaPhlAn2
Version 1

View on GitHub

Download RO-Crate

Run on Galaxy

Workflow Type: Galaxy

Work-in-progress

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/

SEEK ID: https://workflowhub.eu/workflows/624?version=1

DOI: 10.48546/workflowhub.workflow.624.1

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

Frozen Version-1 773b595

Creators and Submitter

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

Valentine Murigneux

Citation

Murigneux, V., Thang, M., Hiltemann, S., & Batut, B. (2024). Analyses of shotgun metagenomics data with MetaPhlAn2. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.624.1

License

Creative Commons Attribution 4.0 International

Activity

Views: 4018 Downloads: 460 Runs: 0

Created: 26th Oct 2023 at 20:34

Last updated: 14th Nov 2023 at 21:43

Annotated Properties

Topic annotations

Metagenomics, Metagenomic sequencing

Operation annotations

Taxonomic classification

Analyses of shotgun metagenomics data with MetaPhlAn2 Version 1