Simple, scalable genotyping and copy number data analysis

Axiom Analysis Suite integrates single nucleotide polymorphism (SNP) genotyping, insertion/deletion (indel) detection, multiallele analysis, and off-target variant (OTV) calling of simple and complex genomes as well as copy number detection in an easy-to-use graphical interface. The software automates 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 visualization capabilities.

Download the latest version of the Axiom Analysis Suite software below and install by following the instructions in the Axiom Analysis Suite User Guide. This version is compatible with Microsoft Windows 10 (64-bit) Professional operating systems and Quad Core 2.83 GHz systems with a recommended 32 GB RAM. In addition, we recommend a minimum of 150 GB of free space on the C drive to run an analysis. 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 5.2 software

Axiom Analysis Suite 5.2 software provides all the capabilities of previous Axiom Analysis Suite versions but includes the following:

  • Improved automated SNP quality control checks as well as enhancements to usability and reporting of results
  • Tools and visualizations needed to perform copy number variation (CNV) analysis in regions with predetermined boundaries (i.e., fixed-region analysis) and across the entire genome (i.e., discovery analysis)
  • New workflows for making high-quality copy number reference files that get the best results for CNV analysis. The new workflows are supported for a subset of copy number-enabled Axiom arrays.
AxAS 5.2_rev.Fig1

Figure 1. (A) Best Practices Copy Number Reference Creation step 1 batch, marking likely copy neutral samples to make a copy number reference. (B) The step 2 batch tests the new copy number reference on same data. Copy neutral samples should have a MedianLog2Ratio centered at 0.

For a complete list of changes, please see the latest release notes. 

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.

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For Research Use Only. Not for use in diagnostic procedures.