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bcl2fastq website  

bcl2fastq conversion software can be used to both demultiplex data and convert BCL files to FASTQ files. This software requires a Linux operating system. The bcl2fastq2 software can be used to convert BCL files from all Illumina sequencing systems running RTA version 2.0 and above. This is a change from the original information, which indicated that v2.16 could be used with all sequencers running RTA 1.18 and above: that information is no longer correct. For conversion of data generated on Illumina sequencing systems using versions of RTA before RTA 2.0, use bcl2fastq v1.8.4.

Required Modules


  • bcl2fastq

System Variables

  • HPC_BCL2FASTQ_DIR - installation directory


  • Validate 4/5/2018