The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

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ID: 291521
2009
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Abstract
FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open Bioinformatics Foundation projects Biopython, BioPerl, BioRuby, BioJava and EMBOSS. Being an open access publication, it is hoped that this description, with the example files provided as Supplementary Data, will serve in future as a reference for this important file format.
Reference Key
openalex_W2117608012 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Peter Cock, Christopher J. Fields, N. Goto, Michael Heuer, Peter M. Rice
Journal Nucleic Acids Research
Year 2009
DOI
10.1093/nar/gkp1137
URL
https://academic.oup.com/nar/article-pdf/38/6/1767/16769834/gkp1137.pdf
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