8.2. Convert Sequencing Data to FASTQ Format

bcl2fastq2 converter is used to demultiplex sequencing data and convert base call (BCL) files to FASTQ files. The user manual can be downloaded from the following link:

https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf

Find the list of dual indexes in Appendix D or Example sample sheet (Right-click link and select Save Link As… to save .txt file)

*This step can be overlooked if demultiplexed fastq files were generated from NGS sequencing core.