ASSIsT: an automatic SNP scoring tool for in- and outbreeding species
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Author
Di Guardo, Mario
Bianco, Luca
Koehorst-van Putten, Herma J. J.
Longhi, Sara
Costa, Fabrizio
Velasco, Riccardo
Troggio, Michela
van de Weg, Eric W.
Publication date
2015-08-06ISSN
1367-4803
Abstract
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
575 - General genetics. General cytogenetics
Pages
2
Publisher
Oxford University Press
Is part of
Bioinformatics
Citation
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.
Grant agreement number
EC/FP7/265582/EU/Integrated approach for increasing breeding efficiency in fruit tree crops/FRUIT BREEDOMICS
Program
Genòmica i Biotecnologia
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2850]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by-nc/4.0/