Workflow Type:  Galaxy
        
  
            
              
                
                     
                
              
            
        
          
            
              
    
      
        
        
    
            
          
        
        
      
  
    
      
        
      
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This workflow extracts protein-coding sequences from whole genome sequencing (WGS) data obtained from the European Nucleotide Archive (ENA). It automates the preprocessing, annotation, and selection of relevant protein sequences using tools such as Prokka, FASTA-to-Tabular, and pattern-based selection. The resulting dataset supports downstream analyses including comparative genomics, phylogenetics, and functional annotation.
Steps
| ID | Name | Description | 
|---|---|---|
| 2 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 | 
| 3 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2 | 
| 4 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 | 
| 5 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 | 
| 6 | Shovill | toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2 | 
| 7 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 | 
| 8 | Prokka | toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.6+galaxy1 | 
| 9 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 | 
| 10 | Select | Grep1 | 
Version History
Version 1 (earliest) Created 30th Jun 2025 at 10:26 by Crist John Pastor
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Views: 999 Downloads: 148 Runs: 1
Created: 30th Jun 2025 at 10:26
Annotated Properties
  Topic annotations
  Drug discovery, Immunology, Drug development, Immunoproteins and antigens, Immunoinformatics, Biochemistry, Data mining, Proteins
  
  Operation annotations
  
  
  
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 https://orcid.org/0000-0001-5796-3068
 https://orcid.org/0000-0001-5796-3068
