Visualize and analyze data generated by all of Illumina's platforms with GenomeStudio Data Analysis Software. This powerful informatics solution supports the primary analysis of sequence-based data produced by the Genome Analyzer and microarray-based data generated by the iScan System and BeadXpress Reader. Performance optimized tools and a user-friendly graphical interface allow you to quickly and easily convert data into meaningful results.


Flexible Informatics Solution

The GenomeStudio Software package comprises seven discrete application modules that enable you to conveniently compare data from different applications to obtain a comprehensive view of the genome, gene expression, and regulation. The software's modular nature allows new applications to be added as necessary.

Data generated by Illumina's platforms can be easily exported to a number of third-party software tools for more secondary or tertiary analysis through the use of plug-ins integrated within the GenomeStudio module architecture.

GenomeStudio Software Modules
DNA Sequencing Module
  • Visualize data for single and paired-end DNA sequencing experiments
  • Visualize alignment of stacked reads against a reference genome
  • Match discovered cSNPs with dbSNPs via reports

DNA Sequencing
Module Display

GenomeStudio DNA Sequencing Module Click to enlarge

GenomeStudio displays SNPs identified by CASAVA based on alignment of reads against a reference sequence using the Illumina Chromosome Browser.

The DNA Sequencing (DS) Module empowers efficient data analysis for whole-genome sequencing and resequencing experiments performed using the Genome Analyzer. It displays genome-wide consensus alignments using single-read and paired-end sequencing data as well as SNP discovery and validation experiments using output files generated in the CASAVA module of the Genome Analyzer Pipeline analysis software.

From Discovery to Validation

Import SNPs identified in DNA Sequencing experiments into Illumina's Assay Design Tool (ADT) and match called SNPS against the dbSNP database to identify novel SNPs. An ADT report with the genomic regions containing identified SNPs can be sent to Illumina, who can help you with the design of custom GoldenGate and Infinium genotyping assays.

DS Module Highlights

  • Visualize consensus reads in the reassembled genome
  • Discover and confirm SNPs
  • Monitor coverage
  • Scan and explore results at any level-from single nucleotide to whole genome
RNA Sequencing Module
  • Visualize aligned reads to a reference sequence, splice junction sets, abundant sequence set, etc.
  • Analyze and visualize results of counts of exons, genes and splice junctions found in sample data
  • Jump from table to genome viewer/chromosome browser interactively

RNA Sequencing
Module Display

GenomeStudio RNA Sequencing Module Click to enlarge

GenomeStudio displays aligned sequencing reads against a reference genome in the Illumina Chromosome Browser. The yellow (foward) and blue (reverse) reads cover exons. The splice junctions are indicated in gray.

The RNA Sequencing (RS) Module supports data analysis for transcriptome sequencing and full-length mRNA sequencing experiments performed using the Genome Analyzer system. Using output files from the CASAVA module of the Genome Analyzer Pipeline Software, the RS Module enables you to view regions with interesting expression levels, splice variants, or SNPs.

From Discovery to Validation

Import SNPs identified in RNA Sequencing experiments into Illumina's Assay Design Tool (ADT) and match called SNPS against the dbSNP database to identify novel SNPs. An ADT report with the genomic regions containing identified SNPs can be sent to Illumina, who can help you with the design of custom GoldenGate and Infinium genotyping assays.

RS Module Highlights

  • Perform whole transcriptome analysis
  • Visualize consensus reads in the transcriptome
  • Discover and confirm cSNPs
  • Visualize and analyze expressed genes, exons and splice variants
  • Align to known abundant sequences, a reference genome, and splice junctions
  • Aggregate data from multiple lanes of a flow cell, and count the abundance of reads falling within specific exons, genes, and splice junctions
ChIP Sequencing Module
  • Map global binding sites for DNA-associated proteins
  • Identify differential binding levels between experimental groups

ChIP Sequencing
Module Display

GenomeStudio ChIP Sequencing Module Click to enlarge

Stacked plot of sequence reads for peak and region detection in the GenomeStudio ChIP Sequencing Module.

The ChIP Sequencing (CS) Module supports the analysis of Whole-Genome Chromatin Immunoprecipitation Sequencing (ChiP-Seq) experiments performed using the Genome Analyzer system. Easily transfer sequence data from the Genome Analyzer Pipeline into the CS Module, where you can derive biological meaning from the aligned sequence reads.

The GenomeStudio Framework displays data output in tabular form and enables you to quickly and easily visualize your results using the Illumina Genome Viewer and Illumina Chromosome Browser graphical tools. Nearby genomic elements can also be displayed in the genome browser to facilitate data analysis.

CS Module Highlights

  • Map global binding sites for DNA-associated proteins
  • Identify differential binding levels between experimental groups
  • Transfer sequence data from Pipeline output
  • Align and visualize sequence reads against genome browser
  • Scan and explore results at any level-from single nucleotide to whole genome
  • Combine multiple experiments in a single ChIP-Seq project to maximize coverage
Genotyping Module
  • Analyze SNP and CNV data across 2.1 million markers and probes
  • Detect sample outliers

Genotyping Module Display

GenomeStudio Genotyping Module Click to enlarge

The graphical display of genotypes in GenomeStudio is a Genoplot, with data points color coded for the call (red = AA, purple = AB, blue = BB). Genotypes are called for each sample (dot) by their signal intensity (norm R) and Allele Frequency (Norm Theta) relative to canonical cluster positions (dark shading) for a given SNP marker.

The GenomeStudio Genotyping (GT) Module supports the analysis of Infinium and GoldenGate Genotyping Assay data collected by the iScan System and BeadXpress Reader. This module enables efficient genotyping data normalization, genotype calling, clustering, data intensity analysis, loss of heterozygosity (LOH) calculation, and copy number variation (CNV) analysis. Fully integrated with Infinium LIMS server, the GT Module allows you to directly access data and manage projects from within GenomeStudio.

As in all GenomeStudio modules, the GenomeStudio Framework displays data output in tabular form and enables you to quickly and easily visualize your results using the Illumina Genome Viewer and Illumina Chromosome Browser graphical tools.

GT Module Highlights

  • Analyze SNP and CNV data across 2.1 million markers
  • Estimate Log R ratio and B-allele frequency for copy number analysis
  • Call genotypes, normalize and cluster data, and generate SNP statistics
  • 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
  • Analyze data from two different product versions within the same project
Gene Expression Module
  • Analyze differentially expressed genes across different genomes
  • Profile miRNA expression
  • Combine mRNA and microRNA data in a single project

Gene Expression
Module Display

GenomeStudio Gene Expression Module Click to enlarge

This head map dendrogram clusters rows (Target ID) and columns (Differential Scores). Using the Heat Map tools in the GX Module allows easy visualization and analysis of large amounts of data.

The GenomeStudio Gene Expression (GX) Module supports the analysis of Direct Hyb and DASL Assay data collected by the iScan System and BeadXpress Reader. This module allows you to visualize differential mRNA and microRNA expression analysis as line plots, histograms, dendrograms, box plots, heat maps, scatter plots, samples tables, and gene clustering diagrams. Simplified data management tools in GenomeStudio Software include hierarchical organization of samples, groups, group sets, and all associated project analysis.

As in all GenomeStudio modules, the GenomeStudio Framework displays data output in tabular form and enables you to quickly and easily visualize your results using the Illumina Genome Viewer and Illumina Chromosome Browser graphical tools.

GX Module Highlights

  • Analyze differential expression using gene-level statistical analysis tools
  • Visualize results as line plots, histograms, dendrograms, box plots, heat maps, scatter plots, samples tables, and gene clustering diagrams
  • Simplify data management for hierarchical organization of samples, groups, group sets, and project analysis
  • Identify fold-level changes, perform T-test and ANOVA and compare results across different sample group sets
  • Combine and merge gene expression data with DNA methylation and miRNA profiling data within same project
  • Export whole-genome expression and genotyping data to various third party tools for eQTL analysis
Methylation Module
  • Detect cytosine methylation at single-base resolution
  • Identify methylation signatures across the entire genome

Methylation Module Display

GenomeStudio Methylation Module Click to enlarge

The GenomeStudio Methylation (M) module supports the analysis of Infinium and GoldenGate Methylation Assay data collected by the iScan System and BeadXpress Reader. This module calculates methylation levels (beta values) and analyzes differential methylation levels between experimental groups and allows you to view CpG island methylation status across the genome with the llumina Genome Browser and Chromosome Browser.

Single-site resolution data can be visualized as line plots, bar graphs, scatter plots, histograms, dendrograms, box plots, or heat maps. This module also enables you to combine methylation data with gene expression profiling experiments within the same GenomeStudio project for correlation between levels of methylated sites (beta values) and differential gene expression levels (p values).

M Module Highlights

  • 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
  • Merge gene expression profiling data with methylation data in the same project
  • Display whole-genome data and beta values within the Illumina Genome Viewer
  • Visualize beta values for one or more samples in the Illumina Chromosome Browser
Protein Analysis Module
  • Analyze immuno-protein assays

Protein Analysis
Module Display

GenomeStudio Protein Analysis Module Click to enlarge

The GenomeStudio Protein Analysis (PT) module supports the analysis of data generated using Carboxyl VeraCode Beads on the BeadXpress Reader. This module allows you to determine analyte concentration using a standards curve, or differential protein expression levels between samples. If applicable, protein levels can be compared to mRNA expression levels. Results can be visualized as line plots, histograms, dendrograms, box plots, heat maps, scatter plots, samples tables, and gene clustering diagrams.

PT Module Highlights

  • Analyze differential protein levels and compare to mRNA expression levels
  • Visualize results as line plots, histograms, dendrograms, box plots, heat maps, scatter plots, samples tables, and gene clustering diagrams

GenomeStudio Software Highlights
Integrated Analysis Analyze data generated from all Illumina Platforms - the Genome Analyzer, iScan System, and BeadXpress Reader
Multi-Assay Analysis Combine data from more than one assay type in the same project; analyze data from a variety of applications using the same program
Powerful Framework Display data output in tabular form; quickly and easily visualize your results using the Illumina Genome Viewer (IGV) and Illumina Chromosome Browser (ICB) graphical tools
Sophisticated Analysis Platform Access high-performance algorithms and statistics calculations that support a wide range of applications
Open Access Export data into a variety of formats compatible with other commercially available analysis tools
Flexible Add plug-ins as new features become available
GenomeStudio System Requirements
ParameterSequencing Data AnalysisMicroarray Data AnalysisMicroarray and Sequencing Data Analysis
CPU Speed Intel Pentium 2.0 GHz or faster Intel Celeron Duo or faster Intel Celeron Duo or faster
Processor 32-bit or 64-bit 64-bit* 64-bit
Memory Size 2 GB or more 4 GB or more 4 GB or more
Hard Drive 250 GB or larger 100 GB or larger 250 GB or larger
Video Display 1,280 x 1,024 1,280 x 1,024 1,280 x 1,024
Operating System Windows XP SP2 or Vista Windows XP SP2 or Vista Windows XP SP2 or Vista
Specific OS Requirements Microsoft .NET Framework 3.5 Microsoft .NET Framework 3.5 Microsoft .NET Framework 3.5
Network Connection 1 GbE or faster 1 GbE or faster 1 GbE or faster

*Gene Expression and Methylation Module data analysis can be performed on 32-bit systems