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Overview of Sequence Data Formats

  • Hongen Zhang
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Sequencing data file format Next-generation sequencing Sequencing data FASTQ FASTA SAM/BAM GFF/GTF BED VCF 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Center for Cancer Research, National Cancer InstituteNational Institutes of HealthBethesdaUSA

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