File formats used in next generation sequencing: A literature review

Abstract

[EN]Next-generation sequencing (NGS) has revolutionized the field of genomics, allowing a detailed and precise look at DNA. As this technology advanced, the need arose for standardized file formats to represent, analyze and store the vast data sets produced. In this article, we review the key file formats used in NGS: FASTA, FASTQ, BED, GFF, and VCF. The FASTA format, one of the oldest, provides a basic representation of genomic and protein sequences, identifiable by unique headers. FASTQ is essential for NGS, as it stores both the sequence and the associated quality information. BED provides a tabular representation of genomic loci, while GFF details the localization and structure of genomic features in reference sequences. Finally, VCF has emerged as the predominant standard for documenting genetic variants, from simple SNPs to complex structural variants. The adoption and adaptation of these formats have been fundamental for progress in bioinformatics and genomics. They provide a foundation on which to build sophisticated analyses, from gene discovery and function prediction to the identification of disease-associated variants. With a clear understanding of these formats, researchers and practitioners are better equipped to harness the power and potential of next-generation sequencing.