Sequencing and Microarray Data Analysis

Illumina’s sequencing and microarray data analysis software packages perform secondary analysis once the on-instrument data processing is complete. These bioinformatics tools ensure optimal time-to-answer, so you can spend more time doing research, and less time configuring and running array and sequencing data analysis workflows.

BaseSpace Core Apps




Tumor Normal

BaseSpace Core Apps include industry-standard workflows for DNA and RNA sequencing data analysis, for the most common Illumina sequencing workflows. Learn more about BaseSpace Core Apps »

HiSeq and Isaac Analysis Software

HiSeq Analysis Software provides alignment and variant calling for whole human genome and exome libraries sequenced on the HiSeq system. Whole human genome sequencing utilizes the Isaac workflow for rapid, accurate sequencing data analysis. Learn more about HiSeq and Isaac Analysis Software »

MiSeq Reporter

On the MiSeq sequencer, after sequencing and primary data analysis, MiSeq Reporter can perform secondary sequencing data analysis directly on the instrument computer. MiSeq Reporter supports multiple biological workflows, and provides data visualization, sample quality analysis and coverage information. Learn more about MiSeq Reporter »

GenomeStudio Software

GenomeStudio Software enables you to conveniently visualize and analyze sequencing and microarray data generated on Illumina's platforms. The software package is comprised of seven discrete application modules. Learn more about GenomeStudio Software »

KaryoStudio Software

KaryoStudio software performs cytogenetic microarray data analysis in a user-friendly interface. KaryoStudio supports data analysis for Illumina's Infinium HD BeadChips. Learn more about KaryoStudio Software »

Beeline Software

As the size of experimental microarray data sets increases, the time required to calculate sample statistics and visually interrogate clusters has become prohibitive. Beeline software addresses this bottleneck, and offers a direct path to microarray data analysis. Learn more about Beeline Software »

BaseSpace Apps

BaseSpace offers a wide variety of free and paid sequencing data analysis apps. Learn more about
BaseSpace Apps »

IGN Sequencing Data Analysis Services

Illumina Genome Network (IGN) offers highly accurate human whole-genome sequencing and data analysis services. 
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Easily Analyze RNA-Seq Data

Our RNA-Seq data analysis tools are accessible to any researcher, regardless of bioinformatics experience.

Sequencing Data Analysis Training

Learn more about options for analyzing your sequencing data. 
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Variant Analysis for Clinical Researchers

Quickly identify and classify clinically relevant disease variants in sequencing data with VariantStudio Software. 
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How to Analyze Microarray Data

Access online training modules to learn how to analyze your array data with Illumina software.
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For Research Use Only.