Metagenomic GEMs from Assembly Version 1
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Download RO-CrateWorkflow for Metagenomics from bins to metabolic models (GEMs)
Summary
- Prodigal gene prediction
- CarveMe genome scale metabolic model reconstruction
- MEMOTE for metabolic model testing
- SMETANA Species METabolic interaction ANAlysis
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here:
Tools: https://gitlab.com/m-unlock/cwl
Workflows: https://gitlab.com/m-unlock/cwl/workflows
How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html
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Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | Identifier used | Identifier for this dataset used in this workflow |
|
| bins | Genome/bin | Bin/genome fasta files |
|
| solver | n/a | Solver to be used in MEMOTE and SMETANA (defaul; cplex) |
|
| threads | number of threads | Number of threads to use for computational processes |
|
| destination | Output Destination (prov only) | Not used in this workflow. Output destination used for cwl-prov reporting only. |
|
Steps
| ID | Name | Description |
|---|---|---|
| prodigal | prodigal | prodigal gene/protein prediction |
| compress_prodigal | Compress proteins | Compress prodigal protein files |
| carveme | CarveMe | Genome-scale metabolic models reconstruction with CarveMe |
| compress_carveme | Compress GEM | Compress CarveMe GEM |
| gemstats | GEM stats | CarveMe GEM statistics |
| smetana | SMETANA | Species METabolic interaction ANAlysis |
| memote_report_snapshot | MEMOTE report snapshot | Take a snapshot of a model's state and generate a report. |
| memote_run | MEMOTE report snapshot | MEMOTE run analsis |
| carveme_files_to_folder | CarveMe GEMs to folder | Preparation of workflow output files to a specific output folder |
| prodigal_files_to_folder | Prodigal proteins to folder | Preparation of workflow output files to a specific output folder |
| memote_files_to_folder | MEMOTE output | Preparation of workflow output files to a specific output folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| carveme_gems_folder | CarveMe GEMs folder | CarveMe metabolic models folder |
|
| protein_fasta_folder | Protein files folder | Prodigal predicted proteins (compressed) fasta files |
|
| memote_folder | MEMOTE outputs folder | MEMOTE outputs folder |
|
| smetana_output | SMETANA output | SMETANA detailed output table |
|
| gemstats_out | GEMstats | CarveMe GEM statistics |
|
Version History
Version 1 (earliest) Created 7th Jul 2022 at 09:23 by Bart Nijsse
Initial commit
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masterdfc8e9c
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Views: 3897 Downloads: 620
Created: 7th Jul 2022 at 09:23
Last updated: 2nd Nov 2022 at 15:41
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Teams: UNLOCK, Systems and Synthetic Biology
Organizations: UNLOCK, Wageningen University & Research
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