# 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. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/fastq-generation.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.