Microarray Analysis Software for Agrigenomics

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Advancing agrigenomics with quality and trusted results

 

Scientists and researchers around the world are leveraging microarray technology to advance agrigenomics in plants and animals, uncovering critical genetic insights related to disease resistance, productivity, and adaptation. These tools are accelerating discoveries in breeding, health, and sustainability across diverse species.

 

With our microarray software suite, you can uncover agriculturally relevant insights in agrigenomics through powerful data analysis, mining, and management tools—enabling deeper understanding of genetic traits in plants and animals for improved breeding, disease-resistance, and productivity.

Axiom Analysis Suite software

Axiom Analysis Suite software 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.

 

Axiom Analysis Suite integrates the following in an easy-to-use interface:

  • Single nucleotide polymorphism (SNP) genotyping
  • Insertion/deletion (indel) detection
  • Multi-allele analysis
  • Off-target variant (OTV) calling of simple and complex genomes
  • Copy number detection

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 extract copy number information with newly added visualization capabilities.

Axiom Analysis Suite 5.4

Improved genotyping, for difficult markers in multiplate batches

 

Recent updates include:

  • AxAS Best Practices and Genotyping Analysis now includes remote copy number when the library package includes remote copy number genotyping. These algorithms increase accuracy for genes that have been previously difficult to call.

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.

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.

Automated Axiom Analysis Software

This software package enables analysis of the CEL files upon scan completion of an Axiom array plate on the GeneTitan MC instrument without user intervention.

 

Upon completion of plate scanning, a notification is sent to the Application Server Core and sample files are automatically uploaded to a designated folder. The Core alerts the Automated Axiom Analysis Software that CEL files are available for analysis. Automated Axiom then runs the analysis based on the default workflow that has been pre-selected for that specific array type. The results are stored in an Axiom Analysis Suite v5.0 or higher batch folder.

Axiom Batch SSP Tool

This software package enables creation of SNP-specific priors for your custom array. Benefits of utilizing SNP-specific priors are increased data robustness and batch-to-batch reproducibility.  The Axiom Batch SSP Tool uses an analyzed batch of CEL files as input and produces outputs easily incorporated into subsequent analysis batches.

 

To access the Axiom Batch SSP Tool, contact your microarray Field Application Specialist.

Axiom Long Export Format Tool (AxLE)

The Axiom Long Export Format Tool (AxLE) is a companion software application to Axiom Analysis Suite software that enables the export of Axiom array genotyping data into long format for easy comparison to legacy arrays.

 

Features include:

  • Separate drop-down sections for Template, Input File, and Export Settings
  • Enhanced Template functionality
  • Ability to save specified Input files, export options, and selected Export files in on configuration
  • Ability to group samples into separate export files
  • Templates for Sample Filter and Sample Grouping

 

Benefits include:

  • Easy to use software tool
  • Helps reduce the need to change existing bioinformatics pipelines
  • For use with both human and non-human Axiom arrays
  • Standardized nomenclature for International Society of Animal Genetics (ISAG)
  • Enables alignment with breed associations for trait evaluations

 

The AxLE Tool requires Axiom Analysis Suite software to be installed prior to use. It is supported by 64-bit Microsoft Windows 10 Professional.

 

The AxLE Tool cannot be used for analyzing data from the Genome-Wide Human SNP Array 6.0 and can only be used for data from Axiom genotyping arrays.

Axiom CNV Summary Tools Software

The Axiom CNV summary tools use intensity and genotypes to calculate log2 ratios and B allele frequencies from genotyping data.

Eureka Analysis Suite Software

Eureka Analysis Suite software is designed for automated data analysis of agriculture genotyping applications.

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