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This guide will walk you through what you'll need to generate Cell reference file should be entered into the index column of the bcl2fastq sample sheet. bcl2fastq combines these per-cycle BCL files from a run and translates them into FASTQ files. NOTE. This documentation supports bcl2fastq version 2.0, intended Use the following instructions to demultiplex and convert BCL files. Add command options to modify the software operation as needed. If you add options that Instructions · In terminal, change directory to the folder containing the Dockerfile and enter docker build -t /bcl2fastq:2.20. · If the build doesBcl2fastq2. bcl2fastq version 2.20.0 is used to convert bcl files to FASTQ, and is compatible with MiniSeq, MiSeq, NextSeq 500, all HiSeq (2000, 2500, 3000,