FASTQ

FASTQ is a text-based format used to store nucleotide sequences generated by high-throughput sequencing instruments together with their corresponding quality scores. It is the de facto standard input format for many sequencing pipelines, serving as the primary source for read alignment, genome assembly, and variant calling.

A FASTQ file comprises records that are organized in four lines per read: a header line that starts with an at sign (@) followed by an optional description, a sequence line containing the nucleotide bases, a third line that starts with a plus sign (+) and may include an optional description, and a fourth line with quality scores encoded as ASCII characters. The quality string must have the same length as the sequence, with one quality character per base.

Quality scores in FASTQ encode the confidence of each base call. Each character represents a Phred quality score, which relates to the probability of an incorrect base call by the formula Q = -10 log10(P_error). The encoding used is typically Phred+33 for most modern data, meaning 33 is added to the score and converted to an ASCII character. Older data may use Phred+64 or other encodings. Because encodings differ, it is important to know the specific quality encoding when interpreting FASTQ files.

FASTQ files can be very large and are frequently stored in compressed form (for example, with the .fastq.gz extension). They are widely supported by quality control and processing tools such as FastQC for assessment, and by trimming, alignment, and assembly tools in sequencing workflows. The format’s combination of sequence data and per-base quality information facilitates error modeling and filtering throughout genomic analyses.