What Are FASTQ Files?

. A FASTQ file is a text-based file format that contains information about the read, sequence data from clusters that pass filter, and a quality value for each base in the sequence.

One FASTQ file is generated for each lane of the flow cell and for each read in the sequencing run. For example, a single-read run on one four-lane flow cell generates four FASTQ files. A paired-read run on the same flow cell generates eight FASTQ files.

For indexed libraries, a demultiplexing step first assigns clusters to a sample based on the index sequences reported in the sample sheet. After demultiplexing, FASTQ files are then generated for each sample in a lane.

FASTQ files use a compressed format with the extension *.fastq.gz and can be several megabytes or gigabytes in size. They are used as input for performing downstream analysis, such as alignment and assembly.