Flapjack--graphical genotype visualization

Iain Milne, Paul Shaw, Gordon Stephen, Micha Bayer, Linda Cardle, William T B Thomas, Andrew J Flavell, David Marshall*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

96 Citations (Scopus)

Abstract

SUMMARY: New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features.

AVAILABILITY: Flapjack is freely available for Microsoft Windows, Mac OS X, Linux and Solaris, and can be downloaded from http://bioinf.scri.ac.uk/flapjack .

Original languageEnglish
Pages (from-to)3133-4
Number of pages2
JournalBioinformatics (Oxford, England)
Volume26
Issue number24
DOIs
Publication statusPrint publication - 15 Dec 2010
Externally publishedYes

Fingerprint

Quantitative Trait Loci
Chromosomes
Nucleotides
Polymorphism
Genotype
Genetic Markers
Sorting
Single Nucleotide Polymorphism
Navigation
Real-time Rendering
Software
Visualization
Throughput
Technology
Phenotype
Single nucleotide Polymorphism
Large Data
Linux
Software Tools
Sequencing

Keywords

  • Chromosome Mapping
  • Computer Graphics
  • Genotype
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci
  • Software

Cite this

Milne, I., Shaw, P., Stephen, G., Bayer, M., Cardle, L., Thomas, W. T. B., ... Marshall, D. (2010). Flapjack--graphical genotype visualization. Bioinformatics (Oxford, England), 26(24), 3133-4. https://doi.org/10.1093/bioinformatics/btq580
Milne, Iain ; Shaw, Paul ; Stephen, Gordon ; Bayer, Micha ; Cardle, Linda ; Thomas, William T B ; Flavell, Andrew J ; Marshall, David. / Flapjack--graphical genotype visualization. In: Bioinformatics (Oxford, England). 2010 ; Vol. 26, No. 24. pp. 3133-4.
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abstract = "SUMMARY: New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features.AVAILABILITY: Flapjack is freely available for Microsoft Windows, Mac OS X, Linux and Solaris, and can be downloaded from http://bioinf.scri.ac.uk/flapjack .",
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Milne, I, Shaw, P, Stephen, G, Bayer, M, Cardle, L, Thomas, WTB, Flavell, AJ & Marshall, D 2010, 'Flapjack--graphical genotype visualization', Bioinformatics (Oxford, England), vol. 26, no. 24, pp. 3133-4. https://doi.org/10.1093/bioinformatics/btq580

Flapjack--graphical genotype visualization. / Milne, Iain; Shaw, Paul; Stephen, Gordon; Bayer, Micha; Cardle, Linda; Thomas, William T B; Flavell, Andrew J; Marshall, David.

In: Bioinformatics (Oxford, England), Vol. 26, No. 24, 15.12.2010, p. 3133-4.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Flapjack--graphical genotype visualization

AU - Milne, Iain

AU - Shaw, Paul

AU - Stephen, Gordon

AU - Bayer, Micha

AU - Cardle, Linda

AU - Thomas, William T B

AU - Flavell, Andrew J

AU - Marshall, David

PY - 2010/12/15

Y1 - 2010/12/15

N2 - SUMMARY: New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features.AVAILABILITY: Flapjack is freely available for Microsoft Windows, Mac OS X, Linux and Solaris, and can be downloaded from http://bioinf.scri.ac.uk/flapjack .

AB - SUMMARY: New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features.AVAILABILITY: Flapjack is freely available for Microsoft Windows, Mac OS X, Linux and Solaris, and can be downloaded from http://bioinf.scri.ac.uk/flapjack .

KW - Chromosome Mapping

KW - Computer Graphics

KW - Genotype

KW - Polymorphism, Single Nucleotide

KW - Quantitative Trait Loci

KW - Software

U2 - 10.1093/bioinformatics/btq580

DO - 10.1093/bioinformatics/btq580

M3 - Article

VL - 26

SP - 3133

EP - 3134

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 24

ER -

Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas WTB et al. Flapjack--graphical genotype visualization. Bioinformatics (Oxford, England). 2010 Dec 15;26(24):3133-4. https://doi.org/10.1093/bioinformatics/btq580