Axiom Analysis Suite advances genotyping data analysis with a single-source software package to enable complete genotyping analysis of all Axiom arrays and copy number analysis on select 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 as well as copy number detection in an easy-to-use graphical interface. Combining the power of Axiom Genotyping Console (GTC), Analysis Power Tools (APT), and SNPolisher, the software automates the Axiom genotyping best-practices workflow to offer accurate results in a single step for export in PLINK, VCF, or TXT formats. Discover and quickly extract copy number information with newly added capabilities.

Download the latest version of Axiom Analysis Suite (version 4.0 (64-bit)) below and install by following the instructions in the Axiom Analysis Suite User Guide. This version is compatible with Microsoft Windows™ 7 Professional (SP 1) and Microsoft Windows 10 (64-bit) Professional operating systems and Quad Core 2.83 GHz systems with a recommended 16 GB RAM. The software cannot be used to analyze data from the Genome-Wide Human SNP Array 6.0 or any other legacy Affymetrix genotyping arrays.


Axiom Analysis Suite 4.0

Run complete genotyping analyses of all Axiom arrays with a single software package. New with Axiom Analysis Suite 4.0, human array designs are enabled for targeted and de-novo copy number discovery in select regions or genome wide with integrated workflows, Copy Number Fixed Regions and Copy Number Discovery. Easily export and visualize copy number variations and regions of LOH in a variety of formats (such as VCF and Integrative Genomics Viewer compatible). Axiom Analysis Suite 4.0 also supports analysis using earlier versions of library files.

Copy number-enabled Axiom catalog arrays can be found here.

For custom array designs, please contact the microarray chip design team at to determine if CNV-specific library files for your array can be generated. A fee may be applied for generating new library files.

Note: Axiom Analysis Suite versions 3.1 and earlier do not support Axiom copy number analysis. 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

  • Select array type and import sample files and their attributes, select workflow, select analysis configuration settings, and set QC thresholds in the updated Analysis Configuration window.
  • Use default settings or customize settings for your specific analysis needs.

Figure 1. Updated Analysis Configuration window. A) Select array type and import .CEL files to be analyzed, B) select workflow (shown here is copy number de novo workflow) and analysis configurations, and C) set QC thresholds using default thresholds or select individual QC thresholds for your specific needs.

Discover and quickly visualize copy number variations

Figure 2. Copy number states for samples across mutliple adjacent regions after running Copy Number Fixed Regions workflow.

Figure 3. IGV visualization of copy number aberrations showing copy number changes (gain on chr2, circled in red), copy number segments track, B-allele frequency, and smooth signal. Results obtained using Copy Number Discovery workflow.

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 (AxLE).
  • Export results in multiple file formats for use in downstream analysis for all or subset of samples.

Figure 4. Complete Axiom Analysis Suite genotyping 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.


Copy number recommended workflow

  • Execute targeted (Copy Number Fixed Regions) or de novo (Copy Number Discovery) workflow on your sample data.
  • Use provided reference or create your own using Copy Number Reference Creation workflow.
  • Quickly export results in multiple file formats for all or subset of samples for further analysis.
  • Visualize copy number data in tool of choice such as Integrative Genomics Viewer.

Figure 5. Complete Axiom Analysis Suite copy number workflow. Streamlined steps for detecting copy number aberrations including LOH calling.

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.

Figure 6. SNP cluster graphs. A & B) Diploid SNP cluster plots, C) SNP cluster plot from an allo-octoploid plant, and D) after OTV genotyping the OTV cluster has been identified and separated from the AB cluster.

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

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