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

• Published in: Bioinformatics (Oxford, England) Vol. 31; no. 23; pp. 3873 - 3874
• Main Authors: Di Guardo, Mario, Micheletti, Diego, Bianco, Luca, Koehorst-van Putten, Herma J J, Longhi, Sara, Costa, Fabrizio, Aranzana, Maria J, Velasco, Riccardo, Arús, Pere, Troggio, Michela, van de Weg, Eric W
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.12.2015
• Subjects: Alleles; Animals; Applications Notes; Genotyping Techniques - methods; Humans; Laboratorium voor Plantenveredeling; Laboratory of Plant Breeding; PBR Biodiversiteit en Genetische Variatie; PBR Biodiversity and genetic variation; PBR Ornamentals, tissue culture and gene transfer; PBR Siergewassen, Tissue Culture; Plant Breeding; Polymorphism, Single Nucleotide; Software; WUR PB Biodiversiteit en Genetische Variatie; WUR PB Siergewassen, Tissue Culture
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btv446

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. The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/. eric.vandeweg@wur.nl.