Workflow Type:  Galaxy
        
  
            
              
                
                     
                
              
            
        
          
            
              
    
      
        
        
    
    
      
        
        
    
            
          
        
        
      
  
    
      
        
      
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Using:
- vadr annotation (virus model must be selected in options)
- vardict variant caller
- coverage depth Provides summarizing files:
- png image of variant calling with annotations and coverage depths
- tsv file with all information of significant variants only
Steps
| ID | Name | Description | 
|---|---|---|
| 0 | FASTA Width | toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2 | 
| 1 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 | 
| 2 | VADR - Viral Annotation DefineR | toolshed.g2.bx.psu.edu/repos/ftouzain/vadr/vadr/0.2.0 | 
| 3 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 | 
| 4 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 | 
| 5 | bcftools mpileup | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy3 | 
| 6 | VarDict | toolshed.g2.bx.psu.edu/repos/iuc/vardict_java/vardict_java/1.8.3+galaxy1 | 
| 7 | Samtools depth | toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2 | 
| 8 | bcftools call | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy3 | 
| 9 | vvv2_display | - png image of variants - tsv file of variants info toolshed.g2.bx.psu.edu/repos/ftouzain/vvv2_display/vvv2_display/0.2.4.0 | 
| 10 | IUPAC consensus | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3 | 
| 11 | majority consensus | Gives consensus with major nucleotides only toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3 | 
Outputs
| ID | Name | Description | Type | 
|---|---|---|---|
| IUPAC_consensus | #main/IUPAC_consensus | n/a | 
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| Majority_consensus | #main/Majority_consensus | n/a | 
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| image of all variants, genes, proteins and coverage depth | #main/image of all variants, genes, proteins and coverage depth | n/a | 
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| tsv file of information for significant variants | #main/tsv file of information for significant variants | n/a | 
 | 
Version History
Version 1 (earliest) Created 19th Jun 2025 at 11:27 by Fabrice Touzain
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     Creators and Submitter
 Creators and SubmitterCreator
Additional credit
This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne
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Views: 1161 Downloads: 167 Runs: 3
Created: 19th Jun 2025 at 11:27
Last updated: 19th Jun 2025 at 11:29
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 https://orcid.org/0000-0002-1103-2425
 https://orcid.org/0000-0002-1103-2425
