FASTQ format (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "FASTQ format" in English language version.

refsWebsite

Global rank English rank

16nih.gov

4^th place

9doi.org

2^nd place

2web.archive.org

1^st place

2seqanswers.com

low place

2semanticscholar.org

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8^th place

1ucdavis.edu

1,873^rd place

1,347^th place

1ucr.edu

1,553^rd place

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1sourceforge.net

1,669^th place

1,290^th place

1elembio.io

low place

1pacbiofileformats.readthedocs.io

low place

1github.com

383^rd place

320^th place

1epi2me.io

low place

1harvard.edu

18^th place

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1worldcat.org

5^th place

1mattmahoney.net

low place

1illumina.com

low place

doi.org

Cock, P. J. A.; Fields, C. J.; Goto, N.; Heuer, M. L.; Rice, P. M. (2009). "The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants". Nucleic Acids Research. 38 (6): 1767–1771. doi:10.1093/nar/gkp1137. PMC 2847217. PMID 20015970.
Huang, W; Li, L; Myers, J. R.; Marth, G. T. (2012). "ART: A next-generation sequencing read simulator". Bioinformatics. 28 (4): 593–4. doi:10.1093/bioinformatics/btr708. PMC 3278762. PMID 22199392.
Pratas, D; Pinho, A. J.; Rodrigues, J. M. (2014). "XS: A FASTQ read simulator". BMC Research Notes. 7: 40. doi:10.1186/1756-0500-7-40. PMC 3927261. PMID 24433564.
Escalona, Merly; Rocha, Sara; Posada, David (2016). "A comparison of tools for the simulation of genomic next-generation sequencing data". Nature Reviews Genetics. 17 (8): 459–69. doi:10.1038/nrg.2016.57. PMC 5224698. PMID 27320129.
Ginart AA, Hui J, Zhu K, Numanagić I, Courtade TA, Sahinalp SC; et al. (2018). "Optimal compressed representation of high throughput sequence data via light assembly". Nat Commun. 9 (1): 566. Bibcode:2018NatCo...9..566G. doi:10.1038/s41467-017-02480-6. PMC 5805770. PMID 29422526.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Zhu, Kaiyuan; Numanagić, Ibrahim; Sahinalp, S. Cenk (2018). "Genomic Data Compression". Encyclopedia of Big Data Technologies. Cham: Springer International Publishing. pp. 779–783. doi:10.1007/978-3-319-63962-8_55-1. ISBN 978-3-319-63962-8. S2CID 61153904.
Numanagić, Ibrahim; Bonfield, James K; Hach, Faraz; Voges, Jan; Ostermann, Jörn; Alberti, Claudio; Mattavelli, Marco; Sahinalp, S Cenk (2016-10-24). "Comparison of high-throughput sequencing data compression tools". Nature Methods. 13 (12). Springer Science and Business Media LLC: 1005–1008. doi:10.1038/nmeth.4037. ISSN 1548-7091. PMID 27776113. S2CID 205425373.
Ochoa, Idoia; Asnani, Himanshu; Bharadia, Dinesh; Chowdhury, Mainak; Weissman, Tsachy; Yona, Golan (2013). "Qual Comp: A new lossy compressor for quality scores based on rate distortion theory". BMC Bioinformatics. 14: 187. doi:10.1186/1471-2105-14-187. PMC 3698011. PMID 23758828.
Hach, F; Numanagic, I; Alkan, C; Sahinalp, S. C. (2012). "SCALCE: Boosting sequence compression algorithms using locally consistent encoding". Bioinformatics. 28 (23): 3051–7. doi:10.1093/bioinformatics/bts593. PMC 3509486. PMID 23047557.

elembio.io

docs.elembio.io

Elembio AVITI FASTQ format specification https://docs.elembio.io/docs/bases2fastq/outputs/#quality-scores

epi2me.io

labs.epi2me.io

"Introduction_to_Fast5_files". labs.epi2me.io. Retrieved 2022-05-19.

github.com

Dorado duplex basecalling guide [duplex-tools: usage with dorado https://github.com/nanoporetech/duplex-tools#usage-with-dorado-recommended]

harvard.edu

ui.adsabs.harvard.edu

Ginart AA, Hui J, Zhu K, Numanagić I, Courtade TA, Sahinalp SC; et al. (2018). "Optimal compressed representation of high throughput sequence data via light assembly". Nat Commun. 9 (1): 566. Bibcode:2018NatCo...9..566G. doi:10.1038/s41467-017-02480-6. PMC 5805770. PMID 29422526.{{cite journal}}: CS1 maint: multiple names: authors list (link)

illumina.com

Illumina Tech Note.http://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote_understanding_quality_scores.pdf

mattmahoney.net

fastqz.http://mattmahoney.net/dc/fastqz/

nih.gov

pubmed.ncbi.nlm.nih.gov

Cock, P. J. A.; Fields, C. J.; Goto, N.; Heuer, M. L.; Rice, P. M. (2009). "The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants". Nucleic Acids Research. 38 (6): 1767–1771. doi:10.1093/nar/gkp1137. PMC 2847217. PMID 20015970.
Huang, W; Li, L; Myers, J. R.; Marth, G. T. (2012). "ART: A next-generation sequencing read simulator". Bioinformatics. 28 (4): 593–4. doi:10.1093/bioinformatics/btr708. PMC 3278762. PMID 22199392.
Pratas, D; Pinho, A. J.; Rodrigues, J. M. (2014). "XS: A FASTQ read simulator". BMC Research Notes. 7: 40. doi:10.1186/1756-0500-7-40. PMC 3927261. PMID 24433564.
Escalona, Merly; Rocha, Sara; Posada, David (2016). "A comparison of tools for the simulation of genomic next-generation sequencing data". Nature Reviews Genetics. 17 (8): 459–69. doi:10.1038/nrg.2016.57. PMC 5224698. PMID 27320129.
Ginart AA, Hui J, Zhu K, Numanagić I, Courtade TA, Sahinalp SC; et al. (2018). "Optimal compressed representation of high throughput sequence data via light assembly". Nat Commun. 9 (1): 566. Bibcode:2018NatCo...9..566G. doi:10.1038/s41467-017-02480-6. PMC 5805770. PMID 29422526.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Numanagić, Ibrahim; Bonfield, James K; Hach, Faraz; Voges, Jan; Ostermann, Jörn; Alberti, Claudio; Mattavelli, Marco; Sahinalp, S Cenk (2016-10-24). "Comparison of high-throughput sequencing data compression tools". Nature Methods. 13 (12). Springer Science and Business Media LLC: 1005–1008. doi:10.1038/nmeth.4037. ISSN 1548-7091. PMID 27776113. S2CID 205425373.
Ochoa, Idoia; Asnani, Himanshu; Bharadia, Dinesh; Chowdhury, Mainak; Weissman, Tsachy; Yona, Golan (2013). "Qual Comp: A new lossy compressor for quality scores based on rate distortion theory". BMC Bioinformatics. 14: 187. doi:10.1186/1471-2105-14-187. PMC 3698011. PMID 23758828.
Hach, F; Numanagic, I; Alkan, C; Sahinalp, S. C. (2012). "SCALCE: Boosting sequence compression algorithms using locally consistent encoding". Bioinformatics. 28 (23): 3051–7. doi:10.1093/bioinformatics/bts593. PMC 3509486. PMID 23047557.

ncbi.nlm.nih.gov

Cock, P. J. A.; Fields, C. J.; Goto, N.; Heuer, M. L.; Rice, P. M. (2009). "The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants". Nucleic Acids Research. 38 (6): 1767–1771. doi:10.1093/nar/gkp1137. PMC 2847217. PMID 20015970.
Huang, W; Li, L; Myers, J. R.; Marth, G. T. (2012). "ART: A next-generation sequencing read simulator". Bioinformatics. 28 (4): 593–4. doi:10.1093/bioinformatics/btr708. PMC 3278762. PMID 22199392.
Pratas, D; Pinho, A. J.; Rodrigues, J. M. (2014). "XS: A FASTQ read simulator". BMC Research Notes. 7: 40. doi:10.1186/1756-0500-7-40. PMC 3927261. PMID 24433564.
Escalona, Merly; Rocha, Sara; Posada, David (2016). "A comparison of tools for the simulation of genomic next-generation sequencing data". Nature Reviews Genetics. 17 (8): 459–69. doi:10.1038/nrg.2016.57. PMC 5224698. PMID 27320129.
Ginart AA, Hui J, Zhu K, Numanagić I, Courtade TA, Sahinalp SC; et al. (2018). "Optimal compressed representation of high throughput sequence data via light assembly". Nat Commun. 9 (1): 566. Bibcode:2018NatCo...9..566G. doi:10.1038/s41467-017-02480-6. PMC 5805770. PMID 29422526.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Ochoa, Idoia; Asnani, Himanshu; Bharadia, Dinesh; Chowdhury, Mainak; Weissman, Tsachy; Yona, Golan (2013). "Qual Comp: A new lossy compressor for quality scores based on rate distortion theory". BMC Bioinformatics. 14: 187. doi:10.1186/1471-2105-14-187. PMC 3698011. PMID 23758828.
Hach, F; Numanagic, I; Alkan, C; Sahinalp, S. C. (2012). "SCALCE: Boosting sequence compression algorithms using locally consistent encoding". Bioinformatics. 28 (23): 3051–7. doi:10.1093/bioinformatics/bts593. PMC 3509486. PMID 23047557.

watson.nci.nih.gov

Using Genome Analyzer Sequencing Control Software, Version 2.6, Catalog # SY-960-2601, Part # 15009921 Rev. A, November 2009 http://watson.nci.nih.gov/solexa/Using_SCSv2.6_15009921_A.pdf^{[dead link‍]}

pacbiofileformats.readthedocs.io

PacBio BAM format specification 10.0.0 https://pacbiofileformats.readthedocs.io/en/10.0/BAM.html#qual

semanticscholar.org

api.semanticscholar.org

Zhu, Kaiyuan; Numanagić, Ibrahim; Sahinalp, S. Cenk (2018). "Genomic Data Compression". Encyclopedia of Big Data Technologies. Cham: Springer International Publishing. pp. 779–783. doi:10.1007/978-3-319-63962-8_55-1. ISBN 978-3-319-63962-8. S2CID 61153904.
Numanagić, Ibrahim; Bonfield, James K; Hach, Faraz; Voges, Jan; Ostermann, Jörn; Alberti, Claudio; Mattavelli, Marco; Sahinalp, S Cenk (2016-10-24). "Comparison of high-throughput sequencing data compression tools". Nature Methods. 13 (12). Springer Science and Business Media LLC: 1005–1008. doi:10.1038/nmeth.4037. ISSN 1548-7091. PMID 27776113. S2CID 205425373.

seqanswers.com

Seqanswer's topic of skruglyak, dated January 2011 website
Illumina Quality Scores, Tobias Mann, Bioinformatics, San Diego, Illumina http://seqanswers.com/forums/showthread.php?t=4721

sourceforge.net

samtools.sourceforge.net

Sequence/Alignment Map format Version 1.0, dated August 2009 PDF

ucdavis.edu

genomecenter.ucdavis.edu

Sequencing Analysis Software User Guide: For Pipeline Version 1.4 and CASAVA Version 1.0, dated April 2009 PDF Archived June 10, 2010, at the Wayback Machine

ucr.edu

illumina.ucr.edu

Sequencing Analysis Software User Guide: For Pipeline Version 1.5 and CASAVA Version 1.0, dated August 2009 PDF^{[dead link‍]}

web.archive.org

Sequencing Analysis Software User Guide: For Pipeline Version 1.4 and CASAVA Version 1.0, dated April 2009 PDF Archived June 10, 2010, at the Wayback Machine
SolexaQA project website

worldcat.org

search.worldcat.org

Numanagić, Ibrahim; Bonfield, James K; Hach, Faraz; Voges, Jan; Ostermann, Jörn; Alberti, Claudio; Mattavelli, Marco; Sahinalp, S Cenk (2016-10-24). "Comparison of high-throughput sequencing data compression tools". Nature Methods. 13 (12). Springer Science and Business Media LLC: 1005–1008. doi:10.1038/nmeth.4037. ISSN 1548-7091. PMID 27776113. S2CID 205425373.