What is a FASTQ file?

A FASTQ file is a standard text-based format used to store raw sequencing data. Each entry contains a sequence identifier, the nucleotide sequence, a separator, and corresponding quality scores encoded as ASCII characters. FASTQ files are essential in bioinformatics pipelines, as they capture both sequence content and read reliability. Foundry treats FASTQ as standard input, running FastQC/MultiQC and downstream alignment or quantification.