The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Open accessAbstract
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.
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Cites
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Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
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Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080
Self-citationBase-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
Cited by
VSEARCH: a versatile open source tool for metagenomics
(2016) · doi:10.7717/peerj.2584 · Cited by 10,773
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt593 · Cited by 4,497
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
Shen, W., Le, S., Li, Y., & Hu, F. (2016) · PLOS ONE · doi:10.1371/journal.pone.0163962 · Cited by 3,380
Leinonen, R., Sugawara, H., Shumway, M., & on behalf of the International Nucleotide Sequence Database Collaboration (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1019 · Cited by 2,746
PANDAseq: paired-end assembler for Illumina sequences
Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G., & Neufeld, J. D. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-31 · Cited by 2,132
Metadata
- Authors
- Cock, P. J. A., Fields, C. J., Goto, N., Heuer, M. L., & Rice, P. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-12-16
- Volume
- 38
- Issue
- 6
- Pages
- 1767-1771
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2117608012
- Cited by
- 1,879
- References
- 5
- FWCI
- 11.28
- Type
- journal article
- Language
- en
- Open access
- gold
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- Cock, P. J. A., Fields, C. J., Goto, N., Heuer, M. L., & Rice, P. M. (2010). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research. https://doi.org/10.1093/nar/gkp1137
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