An Elegant Solution to Automate Data Analysis for Axiom® Genotyping Arrays

The Axiom^® Genotyping Solution from Affymetrix enables large-scale, high-throughput SNP genotyping for agriculture and human genotyping applications. The Best Practices Workflow addresses various challenges presented by plants, animals, and humans including polyploid genomes, highly inbred samples, and high GC content within genes implicated in disease. This workflow is recommended for generating high-quality genotyping data from Axiom^® arrays. The workflow previously required the use of multiple software applications including Genotyping Console^TM, Microsoft Excel, and SNPolisher from Affymetrix.

Affymetrix has developed new Windows based software which replaces Genotyping Console^TM and implements the Best Practices Workflow. The eight-step process is reduced to a single step with the click of one button. The application eliminates the need for multiple software packages making the automated analysis of diploid and polyploid genomes seamless while also generating various QC metrics. The software offers built-in features that include capability to use parameters such as the inbred penalty, automated SNP classification, OTV genotyping, SNP QC classification, and advanced multi-cluster filters. It automatically generates plate heat maps, box plots, scatter plots, and SNP cluster plots. This software is designed to improve the user experience by simplifying the interface and improving ease of use by combining the power of Genotyping Console™, Affymetrix Power Tools, and SNPolisher.

To enable analysis with these features, simply load desired CEL files, select analysis settings, set QC thresholds, and click “Run Analysis”. The software includes default settings for diploid and polyploid genomes, settings can be customized, and it’s compatible with all Axiom^® arrays.