title: Overview of Sequence Data Formats.
abstract: Next-generation sequencing experiment can generate billions of short reads for each sample and processing of the raw reads will add more information. Various file formats have been introduced/developed in order to store and manipulate this information. This chapter presents an overview of the file formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and VCF that are commonly used in analysis of next-generation sequencing data.
authors.affiliation: Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 6138, Bethesda, MD, 20892, USA. hongen.zhang@nih.gov.
authors.forename: Hongen
authors.initials: H
authors.lastname: Zhang
mesh_terms: D019295:Computational Biology / Q000379:methods / Q000592:standards; D023281:Genomics / Q000379:methods; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods / Q000592:standards; D017421:Sequence Analysis / Q000379:methods* / Q000592:standards*
keywords: BED; FASTA; FASTQ; GFF/GTF; Next-generation sequencing; SAM/BAM; Sequencing data; Sequencing data file format; VCF