Informatics Products

GenomeStudio Software

An integrated platform for analyzing Illumina microarray-based genotyping assay data

Introduction to GenomeStudio Software

Visualize and analyze data generated on Illumina array platforms with GenomeStudio Software. This powerful solution supports the genotyping analysis of microarray data. Performance-optimized tools and a user-friendly graphical interface enable you to convert data into meaningful results quickly and easily.

Genotyping data analysis highlights

GenomeStudio Software offers efficient genotyping data normalization, genotype calling, clustering, data intensity analysis, loss of heterozygosity (LOH) calculation, and copy number variation (CNV) analysis. The software uses trusted algorithms to normalize, cluster, and call genotypes.

  • Analyze SNP and CNV data across millions of markers and probes
  • Estimate Log R ratio and B-allele frequency for copy number analysis
  • Call genotypes, generate SNP statistics, normalize and cluster data, and detect sample outliers
  • Export genotype data to various third-party applications; access multiple CNV algorithms and copy number variation analysis tools
  • Generate a chromosomal heat map for examining copy number aberrations across the entire genome for multiple samples

Genotype clustering

The latest version of the GenTrain algorithm in GenomeStudio Software enables accurate genotyping with improved sample intensity normalization and data clustering.

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Methylation data analysis highlights

GenomeStudio Software supports the analysis of Infinium methylation array data. The software calculates methylation levels (beta values) and analyzes differential methylation levels between experimental groups.

  • Detect cytosine methylation at single-base resolution
  • Identify methylation signatures across the entire genome
  • Calculate methylation levels and visualize CpG island information
  • Analyze differential methylation levels between two experimental groups
  • Visualize results as line plots, bar graphs, scatter plots, histograms, dendrograms, box plots, heat maps, or control summary reports

Streamlined polyploid genotyping

GenomeStudio Software enables analysis of genotyping data from both diploid and polyploid organisms to drive biological insights more efficiently. Analyzing data obtained from genotyping polyploid organisms such as wheat and potato requires special considerations that depend on the level and type of ploidy of the organism.


With GenomeStudio Software, analyzing genotypes of polyploid organisms is performed in a streamlined fashion with automated genotype calling. The software allows calling of as many clusters as desired, enabling studies of hexaploid or octoploid species.

Access GenomeStudio Software

Access to GenomeStudio Software is included with Illumina microarrays.

Download GenomeStudio Software

Find support resources

GenomeStudio Software support
Find user guides, computing requirements, FAQs, documentation, and additional technical information.
GenomeStudio Software plug-ins
Access customized plug-ins and algorithms that can parse and analyze array data exported from GenomeStudio Software.

Related software

DRAGEN Array

DRAGEN Array secondary analysis enables accurate, comprehensive, and efficient genotyping, PGx CNV calling, and star allele annotation for Infinium microarrays.

Beeline Software

This software offers flexible filtering capabilities to reduce microarray data size and facilitate analysis for large array experiments.

DesignStudio Custom Assay Designer

This web-based assay design tool makes it easy to create and optimize custom microarray-based genotyping assays.

Speak with a specialist

Contact us to learn more about our software offerings.