> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/fastq-generation.md).

# FastQ Generation

Sequencing data stored in BCL format are demultiplexed through a process that uses the index sequences unique to each sample to assign clusters to the library from which they originated. Each cluster contains two indexes (i7 and i5 sequences, one at each end of the library fragment). The combination of those index sequences are used to demultiplex the pooled libraries.

After demultiplexing, this process generates FASTQ files, which contain the sequencing reads for each individual sample library and the associated quality scores for each base call, excluding reads from any clusters that did not pass filter.


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