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. Combining the power of Axiom Array Power Tools (APT) and SNPolisher, 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 7 Professional (SP 1) and 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 5.1.1 software

Axiom Analysis Suite 5.1.1 software offers high accuracy genotypes for rare variants. This is enabled by a novel genotyping algorithm (rare het adjustment), which refines heterozygous calls for rare variants. The functionality is enabled by default for Axiom human arrays.

For more information on the novel genotyping algorithm and its benefits see the technical note Rare Heterozygous Adjusted Genotyping.

Axiom Analysis Suite 5.1.1 software contains all enhanced features offered with the 5.0.1 version, including copy number visualization and the ability to analyze multialleles, as well as improved export functionalities

Multiallele analysis

  • Analysis of probe sets that can report calls from more than one alternate allele is enabled
  • Summary report includes additional columns that report metrics for multiallele probe sets

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

Note: The PharmacoScan and CarrierScan arrays will continue to be analyzed on Axiom Analysis Suite 4.0 software.

Copy number analysis enhancements

  • Increased sample batch size to 5000 for all copy number workflows
  • Median log2ratio reported for each Discovery Copy Number segment
  • Whole-genome-view visualization that displays copy number aberrations across the genome for copy number-enabled human and agrigenomics Axiom arrays

 Our copy number-enabled Axiom catalog arrays

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.

Enhanced export functionality

  • Single sample per file export option enabled for VCF, PLINK, or text format
  • Ability to include ProbeSet Summary table information when exporting genotyping data in text format
  • Ability to use Alternate Marker Name in lieu of probe set ID
  • Enhanced VCF and PLINK genotype export formats

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

Download software

Technical documentation

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