A FASTQ file is a text-based format used to store raw sequence data and associated quality scores from high-throughput sequencing experiments. Each read is represented in four lines: the first line is a unique identifier starting with "@", the second line is the nucleotide sequence, the third line is a "+" separator (which may contain additional metadata), and the fourth line encodes the per-base quality scores using ASCII characters. These quality scores reflect the confidence in the accuracy of each base call, with higher scores indicating greater confidence. FASTQ files are essential for initial sequence analysis and quality control processes in NGS workflows.
In essence FASTQ file is a FASTA file with associated quality of each nucleotide.