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 GenomeStudio® (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.

Di Guardo, M.; Micheletti, D.; Bianco, L.; Koehorst van Putten, H.J.J.; Longhi, S.; Costa, F.; Aranzana, M.J.; Velasco, R.; Arús, P.; Troggio, M.; van de Weg, E.W. (2015). ASSIsT: an automatic SNP scoring tool for in- and outbreeding species. BIOINFORMATICS, 31 (23): 3873-3874. doi: 10.1093/bioinformatics/btv446 handle: http://hdl.handle.net/10449/32764

ASSIsT: an automatic SNP scoring tool for in- and outbreeding species

Di Guardo, Mario;Micheletti, Diego;Bianco, Luca;Longhi, Sara;Costa, Fabrizio;Velasco, Riccardo;Troggio, Michela;
2015-01-01

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 GenomeStudio® (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.
Settore BIO/11 - BIOLOGIA MOLECOLARE
2015
Di Guardo, M.; Micheletti, D.; Bianco, L.; Koehorst van Putten, H.J.J.; Longhi, S.; Costa, F.; Aranzana, M.J.; Velasco, R.; Arús, P.; Troggio, M.; van de Weg, E.W. (2015). ASSIsT: an automatic SNP scoring tool for in- and outbreeding species. BIOINFORMATICS, 31 (23): 3873-3874. doi: 10.1093/bioinformatics/btv446 handle: http://hdl.handle.net/10449/32764
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/32764
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