Constructing linkage maps in the genomics era with MapDisto 2.0
Motivation: Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation ef...
| Autores principales: | , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2017
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/82887 |
| _version_ | 1855540437392031744 |
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| author | Heffelfinger, Christopher Fragoso, Christopher A. Lorieux, Mathias |
| author_browse | Fragoso, Christopher A. Heffelfinger, Christopher Lorieux, Mathias |
| author_facet | Heffelfinger, Christopher Fragoso, Christopher A. Lorieux, Mathias |
| author_sort | Heffelfinger, Christopher |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Motivation: Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM).
Results: MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface.
Availability and Implementation: The program is available free of charge at mapdisto.free.fr. |
| format | Journal Article |
| id | CGSpace82887 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace828872025-03-13T09:45:34Z Constructing linkage maps in the genomics era with MapDisto 2.0 Heffelfinger, Christopher Fragoso, Christopher A. Lorieux, Mathias chromosome mapping computer software quantitative trait loci genotyping genetic markers programas de ordenador loci de rasgos cuantitativos marcadores genéticos Motivation: Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM). Results: MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface. Availability and Implementation: The program is available free of charge at mapdisto.free.fr. 2017-07-15 2017-07-27T13:40:48Z 2017-07-27T13:40:48Z Journal Article https://hdl.handle.net/10568/82887 en Open Access Oxford University Press Heffelfinger, Christopher; Fragoso, Christopher A.; Lorieux, Mathias. 2017. Constructing linkage maps in the genomics era with MapDisto 2.0 . Bioinformatics 33(14): 2224-2225. |
| spellingShingle | chromosome mapping computer software quantitative trait loci genotyping genetic markers programas de ordenador loci de rasgos cuantitativos marcadores genéticos Heffelfinger, Christopher Fragoso, Christopher A. Lorieux, Mathias Constructing linkage maps in the genomics era with MapDisto 2.0 |
| title | Constructing linkage maps in the genomics era with MapDisto 2.0 |
| title_full | Constructing linkage maps in the genomics era with MapDisto 2.0 |
| title_fullStr | Constructing linkage maps in the genomics era with MapDisto 2.0 |
| title_full_unstemmed | Constructing linkage maps in the genomics era with MapDisto 2.0 |
| title_short | Constructing linkage maps in the genomics era with MapDisto 2.0 |
| title_sort | constructing linkage maps in the genomics era with mapdisto 2 0 |
| topic | chromosome mapping computer software quantitative trait loci genotyping genetic markers programas de ordenador loci de rasgos cuantitativos marcadores genéticos |
| url | https://hdl.handle.net/10568/82887 |
| work_keys_str_mv | AT heffelfingerchristopher constructinglinkagemapsinthegenomicserawithmapdisto20 AT fragosochristophera constructinglinkagemapsinthegenomicserawithmapdisto20 AT lorieuxmathias constructinglinkagemapsinthegenomicserawithmapdisto20 |