title: ASSIsT: an automatic SNP scoring tool for in- and outbreeding species.
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.
  
  
  METHODS
  The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/.
  
  
  BACKGROUND
  eric.vandeweg@wur.nl.
authors.affiliation: Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy, Graduate School Experimental Plant Sciences, Wageningen University, 6700 AJ Wageningen, The Netherlands and.
authors.forename: Mario
authors.initials: M
authors.lastname: Di Guardo
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy, Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands.
authors.forename: Diego
authors.initials: D
authors.lastname: Micheletti
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Bianco
authors.affiliation: Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands.
authors.forename: Herma J J
authors.initials: HJ
authors.lastname: Koehorst-van Putten
authors.affiliation: Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands.
authors.forename: Sara
authors.initials: S
authors.lastname: Longhi
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Costa
authors.affiliation: IRTA, Centre de Recerca en Agrigenómica CSIC-IRTA-UAB, Beellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain.
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Aranzana
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.affiliation: IRTA, Centre de Recerca en Agrigenómica CSIC-IRTA-UAB, Beellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain.
authors.forename: Pere
authors.initials: P
authors.lastname: Arús
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
authors.affiliation: Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands.
authors.forename: Eric W
authors.initials: EW
authors.lastname: van de Weg
mesh_terms: D000483:Alleles; D000818:Animals; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012984:Software