What is the most common file type used in next-generation sequencing (NGS)?

The most common file type used in next-generation sequencing (NGS) is FASTQ. This file format plays a crucial role in the NGS workflow as it contains both the sequence data and the corresponding quality scores for each base in the sequence.

When DNA or RNA undergoes sequencing by NGS technology, the output is typically a representation of millions of short sequences known as reads. The FASTQ format is specifically designed to handle this type of data by providing a standardized way to store both the nucleotide sequences and their quality information in a single file. This quality data is essential for downstream applications, as it allows researchers to assess the reliability of the sequence data.

While other file types such as CSV, XML, and TXT can be used in various contexts, they do not cater specifically to the needs of sequencing data. For example, CSV is often used for structured data in spreadsheet applications; XML is a markup language that defines rules for encoding documents in a format that is both human-readable and machine-readable; and TXT files are plain text files that can comprise various kinds of data but lack the specific structure and quality information required for sequencing data. Hence, the use of FASTQ files is fundamental for managing and analyzing NGS output effectively.