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Statistical Genomics pp 3–17Cite as

Overview of Sequence Data Formats

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1418))

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.

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Author information

Authors and Affiliations

  1. Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 6138, Bethesda, MD, 20892, USA

    Hongen Zhang

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  1. Hongen Zhang
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Correspondence to Hongen Zhang .

Editor information

Editors and Affiliations

  1. Ohio State University, Biomed Informatics, College of Medicine, Columbus, Ohio, USA

    Ewy Mathé

  2. National Cancer Institute, National Institutes of Health, Columbia, Maryland, USA

    Sean Davis

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Zhang, H. (2016). Overview of Sequence Data Formats. In: Mathé, E., Davis, S. (eds) Statistical Genomics. Methods in Molecular Biology, vol 1418. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3578-9_1

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  • DOI: https://doi.org/10.1007/978-1-4939-3578-9_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3576-5

  • Online ISBN: 978-1-4939-3578-9

  • eBook Packages: Springer Protocols

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