ASSIsT: an automatic SNP scoring tool for in- and outbreeding species
Ver/Abrir
Autor/a
Di Guardo, Mario
Bianco, Luca
Koehorst-van Putten, Herma J. J.
Longhi, Sara
Costa, Fabrizio
Velasco, Riccardo
Troggio, Michela
van de Weg, Eric W.
Fecha de publicación
2015-08-06ISSN
1367-4803
Resumen
ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudioV R (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker–trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux.
Tipo de documento
Artículo
Versión del documento
Versión publicada
Lengua
English
Materias (CDU)
575 - Genética general. Citogenética general. Inmunogenética. Evolución. Filogenia
Páginas
2
Publicado por
Oxford University Press
Publicado en
Bioinformatics
Citación
Di Guardo, Mario, Diego Micheletti, Luca Bianco, Herma J. J. Koehorst-Van Putten, Sara Longhi, Fabrizio Costa, Maria J. Aranzana, et al. 2015. “ASSIsT: An Automatic SNP Scoring Tool for In- and Outbreeding Species.” Bioinformatics 31 (23): 3873–74. https://doi.org/10.1093/bioinformatics/btv446.
Número del acuerdo de la subvención
EC/FP7/265582/EU/Integrated approach for increasing breeding efficiency in fruit tree crops/FRUIT BREEDOMICS
Program
Genòmica i Biotecnologia
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