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## convert-bcl-to-fastq.rst

      
        
          
            
              
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                brantfaircloth
                / convert-bcl-to-fastq.rst
            
            
              Created
              July 16, 2012 23:44
            
              
                Convert BCL files to fastq
              
          
        
      
        
  
      
    Install dependencies and Casava

The following assumes you are converting BCL files containing PE100 reads with a 10 nt index read. You can allow Casava to demultiplex for you or do it on your own, later. You can adjust values below if you are doing something different (e.g. shorter reads, longer indexes) but be careful.

You need a pretty beefy machine. Illumina recommends something with multiple cores and 48 GB RAM, running Centos 5. Centos 6 also works just fine. See their recommendations here: