metagenomic-raw-reads-amr-analysis/main
View on GitHub
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Frozen
Tests This workflow starts from metagenomics short-read data and performs, taxonomic profiling (using Sylph), predicts Antibiotic Resistance Genes (ARGs) (using Groot and deepARG), and standardizes ARG annotations (using argNorm).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| ARG Database for DeepARG | ARG Database for DeepARG | Database that will be used by deepARG to predict Antibiotic Resistance Genes (ARGs) |
|
| ARG Database for Groot | ARG Database for Groot | Database that will be used by Groot to type Antibiotic Resistance Genes (ARGs) |
|
| ARG Database used by Groot for ARGnorm | ARG Database used by Groot for ARGnorm | Database used by Groot that will be used by argNorm to normalize the ARG annotations to the ARO. It must be the same one set for Groot. |
|
| Average Read Length for Groot | Average Read Length for Groot | This sets the length of the sequence segments (in base pairs) used to create 'fingerprints' (MinHash sketches) of the ARG variation graphs. It should match the average length of the reads (e.g., 100 bp for short reads). Matching the window size to the read length ensures accurate and efficient alignment of reads to the ARG database during analysis. |
|
| Coverage Threshold for Groot to Report an ARG | Coverage Threshold for Groot to Report an ARG | Groot will report ARGs with a coverage higher than the defined value. For example, when 0.95 is set, Groot will report only ARGs where reads cover 95% of bases. |
|
| Contamination Removal | Metagenomics Reads after Quality Control and Host/Contamination Removal | Metagenomics short-reads after quality control and host/contamination removal as a paired collection of fastqsanger(.gz) files |
|
| Minimum probability for considering a reads as ARG-like in deepARG | Minimum probability for considering a reads as ARG-like in deepARG | deepARG categorizes ARGs into two groups based on probability: detected ARGs (sequences with probability ≥ defined threshold) and potential ARGs (sequences with probability < defined threshold). |
|
| Taxonomic Information Database for Sylph | Taxonomic Information Database for Sylph | Sylph profiling outputs do not have taxonomic information, only genome information. With this database, Sylph can turn standard output into a taxonomic profile. |
|
| Taxonomy Profiling Database for Sylph | Taxonomy Profiling Database for Sylph | Sylph will profile the reads against this database. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 8 | Create text file | This step generates a fallback file in case Groot fails. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2 |
| 10 | Unzip collection | __UNZIP_COLLECTION__ |
| 11 | Extract element identifiers | toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 |
| 12 | sylph profile | toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0 |
| 13 | DeepARG short reads | toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy1 |
| 14 | Concatenate files R1 and R2 | Concatenate files R1 and R2 together to enable analysis with Groot cat1 |
| 15 | Flatten collection | Remove a collection level so that outputs can be taken into account by tooldistillator __FLATTEN__ |
| 16 | argNorm on DeepARG ouput | toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0 |
| 17 | Groot | toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2 |
| 18 | Remove beginning | Removal of the first line because it is not necessary for tooldistillator Remove beginning1 |
| 19 | Relabel identifiers | __RELABEL_FROM_FILE__ |
| 20 | Remove beginning | Removal of the first argNorm line that causes a multiQC error Remove beginning1 |
| 21 | argNorm on Groot output | toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0 |
| 22 | table rename column | Rename #ARG column in ARG because it causes multiQC error toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy1 |
| 23 | Filter failed datasets | __FILTER_FAILED_DATASETS__ |
| 24 | Remove beginning | Removal of the first argNorm line that causes a multiQC error Remove beginning1 |
| 25 | ToolDistillator | toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0 |
| 26 | table rename column | Rename Groot columns because there is no information on initial output toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy1 |
| 27 | ToolDistillator Summarize | toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0 |
| 28 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Sylph sylphmpa Files | Sylph sylphmpa Files | n/a |
|
| Sylph Taxonomy Profiling | Sylph Taxonomy Profiling | n/a |
|
| Sylph Merge Taxonomy | Sylph Merge Taxonomy | n/a |
|
| DeepARG Mapping ARG (>min probability) | DeepARG Mapping ARG (>min probability) | n/a |
|
| DeepARG Mapping Potential ARG ( | DeepARG Mapping Potential ARG ( | n/a |
|
| DeepARG ARG Subtype | DeepARG ARG Subtype | n/a |
|
| DeepARG ARG Type | DeepARG ARG Type | n/a |
|
| DeepARG Merged ARG | DeepARG Merged ARG | n/a |
|
| DeepARG All Hits | DeepARG All Hits | n/a |
|
| Paired end Concatenated | Paired end Concatenated | n/a |
|
| output | output | n/a |
|
| argNorm DeepARG Report | argNorm DeepARG Report | n/a |
|
| Groot Report | Groot Report | n/a |
|
| argNorm Groot Report | argNorm Groot Report | n/a |
|
| Tooldistillator Results | Tooldistillator Results | n/a |
|
| Tooldistillator Summarize | Tooldistillator Summarize | n/a |
|
| MultiQC report | MultiQC report | n/a |
|
Version History
v1.0 (earliest) Created 24th Jan 2026 at 03:01 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0cf35051
Creators and Submitter
Activity
Views: 661 Downloads: 4737 Runs: 0
Created: 24th Jan 2026 at 03:01
TagsThis item has not yet been tagged.
AttributionsNone
Related items
Advanced Spaces list for this Workflow with search and filtering
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
Advanced Teams list for this Workflow with search and filtering
The Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.
You can contribute too!
Space: Galaxy
Public web page: https://iwc.galaxyproject.org/
