BaseSpace Sequence Hub converts *.bcl files into FASTQ files, which contain base call and quality information for all reads that pass filtering.
BaseSpace Sequence Hub automatically generates FASTQ files in sample sheet-driven workflow apps. Other apps that perform alignment and variant calling also automatically use FASTQ files.
FASTQ files can be used as sequence input for alignment and other secondary analysis software. Do not use them with tools that are not compatible with the FASTQ format.