ASSIST

ASSIST automates SNP scoring and filtering for Illumina Infinium arrays and custom genotyping arrays to produce improved genotype calls for genetic mapping and marker–trait association analyses.

Key Features:

• Integration with GenomeStudio®: Processes and leverages output from GenomeStudio® (Illumina) for downstream SNP scoring and filtering.
• Bi-allelic genetic model identification: Identifies markers that conform to a bi-allelic genetic model to support reliable genotype calls.
• Re-editing of SNP calls: Re-edits SNP calls that contain null alleles or additional SNPs in the probe annealing site.
• Population support: Handles diverse population types including full-sib families, backcrosses, F1 and F2 generations, and unrelated individuals.
• Export functionality: Produces output files compatible with software used for genetic mapping and marker–trait association analysis.
• Array specificity: Tailored processing for Illumina Infinium arrays and custom genotyping arrays.

Scientific Applications:

• Plant genetics: Analysis of complex mating schemes and population structures in plant breeding and genetics studies.
• Genetic mapping: Generation of filtered SNP datasets suitable for linkage mapping workflows.
• Marker–trait association studies: Preparation of curated SNP calls for marker–trait association analyses.

Methodology:

Implemented in Python; processes GenomeStudio® output from Illumina Infinium and custom genotyping arrays, identifies bi-allelic markers, re-edits SNP calls with null alleles or probe-site polymorphisms, and exports results to formats for genetic mapping and association software; compatible with Windows and Linux.