Axiom Analysis Suite advances genotyping data analysis with a single-source software package to enable complete genotyping analysis of all Axiom arrays

Axiom™ Analysis Suite integrates single nucleotide polymorphism (SNP) genotyping, insertion/deletion (indel) detection, and off-target variant (OTV) calling of simple and complex genomes in an easy-to-use graphical interface. Combining the power of Axiom Genotyping Console (GTC) software, Affymetrix™ Power Tools (APT), and SNPolisher, the software automates the Affymetrix Best Practices Workflow to deliver accurate results in a single step for export in PLINK, VCF, or TXT formats.

Axiom Analysis Suite 2.0

Run complete genotyping analysis of all Axiom arrays with a single software package.
Axiom Analysis Suite 2.0, the latest release, supports analysis with all earlier versions of Axiom analysis library files.
Note: Axiom Analysis Suite versions 1.1.0 and earlier do not support Axiom analysis library files created after April 2016.

Easy-to-use single click for complete analysis

  • Import sample files, select analysis configuration settings, and set QC thresholds in the New Analysis configuration window.
  • Utilize default settings for diploid and polyploid species, or customize settings for your specific analysis needs.
Figure 1. Axiom Analysis Suite New Analysis configuration window: A) Import .CEL files to be analyzed. B) Select analysis configurations based on sample size with ability to change, save, and share selections for models, gender, inbred, and hints files. C) Set QC Thresholds, utilizing default thresholds for human, diploid, or polyploid species or select individual QC thresholds for your specific needs.
Figure 2. Complete Axiom Analysis Suite workflow: Automatically perform the Axiom Best Practices Workflow including sample and plate QC, genotyping of high-quality samples, SNP clustering, calling and classification. Review QC results, Sample and SNP summary tables, plots of QC metrics, and cluster graphs of individual markers.

Complete genotyping analysis in one package

  • Complete the Best Practices Workflow with the click of one button: perform sample and plate QC, genotype high-quality samples, and filter SNPs into defined classifications.
  • Use default or custom views to visualize results: review plate-level QC heat maps and box plots, evaluate sample performance with box plots and scatter plots, and view individual SNP cluster plots.
  • Interact with external tools for further Axiom analysis (CNV Summary Tool).
  • Export results in multiple file formats for use in downstream analysis.

Automatically categorize SNPs into six main cluster types

  • View SNP cluster graphs which are generated for each marker, allowing a detailed look at the performance of SNPs of interest.
  • Classify each SNP into cluster types for ease of interpretation and to prevent misinterpretation of genotype calls.
  • Manually edit genotype calls for one or more samples for a single marker with the "Change Call" function.

For a complete list of features, please download the latest release notes.

Download the latest version of Axiom Analysis Suite, version 2.0 (64-bit), and install the software by following the installation instructions found in the Axiom Analysis Suite User Guide. This version is supported on Microsoft Windows™ 7 Professional (SP 1) and Microsoft Windows 8.1 (64-bit) Professional, Quad Core System 2.83 GHz with recommended 16 GB RAM. The software cannot be used for analyzing data from Genome-Wide Human SNP Array 6.0 or any other legacy Affymetrix genotyping arrays.

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