Workflow Type:  Galaxy
        
  
        
          
            
              
    
      
        
        
    
    
      
        
        
    
            
          
        
        
      
  
    
      
        
      
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Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Metabarcoding/eDNA through Obitools" .
This workflow allows to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools.
Inputs
| ID | Name | Description | Type | 
|---|---|---|---|
| wolf_tutorial.zip?download=1 | wolf_tutorial.zip?download=1 | n/a | 
 | 
Steps
| ID | Name | Description | 
|---|---|---|
| 1 | Illuminapairedend | toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13 | 
| 2 | Unzip | toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2 | 
| 3 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 | 
| 4 | FASTQ Groomer | toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 | 
| 5 | obigrep | toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13 | 
| 6 | Line/Word/Character count | wc_gnu | 
| 7 | Line/Word/Character count | wc_gnu | 
| 8 | NGSfilter | toolshed.g2.bx.psu.edu/repos/iuc/obi_ngsfilter/obi_ngsfilter/1.2.13 | 
| 9 | obiuniq | toolshed.g2.bx.psu.edu/repos/iuc/obi_uniq/obi_uniq/1.2.13 | 
| 10 | obiannotate | toolshed.g2.bx.psu.edu/repos/iuc/obi_annotate/obi_annotate/1.2.13 | 
| 11 | obistat | toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13 | 
| 12 | obigrep | toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13 | 
| 13 | obigrep | toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13 | 
| 14 | obiclean | toolshed.g2.bx.psu.edu/repos/iuc/obi_clean/obi_clean/1.2.13 | 
| 15 | NCBI BLAST+ blastn | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0 | 
| 16 | Filter sequences by ID | toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7 | 
| 17 | Filter sequences by ID | toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7 | 
| 18 | obitab | toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13 | 
| 19 | obitab | toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13 | 
| 20 | Join two Datasets | join1 | 
| 21 | Join two Datasets | join1 | 
| 22 | Cut | Cut1 | 
| 23 | Filter | Filter1 | 
Version History
Version 1 (earliest) Created 9th Nov 2023 at 12:41 by Yvan Le Bras
Initial commit
Frozen
 Version-1
Version-1e601ed3
     Creators and Submitter
 Creators and SubmitterCreators
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    Citation
  
  
  Le Bras, Y., & Royaux, C. (2024). Obitools eDNA metabarcoding. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.655.1
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Views: 6233 Downloads: 564 Runs: 1
Created: 9th Nov 2023 at 12:41
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