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 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 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 »
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 »
Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software performs alignment and variant calling (SNPs and indels) to analyze whole genome sequencing data from all iGenome-supported organisms. CASAVA also supports Nextera dual indexing. Learn more about CASAVA »
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 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 »
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 offers a wide variety of free and paid sequencing data analysis apps. Learn more about BaseSpace Apps »
Illumina Genome Network (IGN) offers highly accurate human whole-genome sequencing and data analysis services.
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Our RNA-Seq data analysis tools are accessible to any researcher, regardless of bioinformatics experience.
These Illumina Genome Network (IGN) webinars describe the full range of whole-genome sequencing data analysis options.
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Quickly identify and classify clinically relevant disease variants in sequencing data with VariantStudio Software.
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Access online training modules to learn how to analyze your array data with Illumina software.
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