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Illumina Connect

Illumina Connect

illumina•Connect is a forum for sharing innovative solutions that enhance the analysis and management of Illumina sequencing and BeadArray data. Illumina’s open architecture software allows third-party vendors to develop powerful new tools that complement and expand data analysis, enabling a faster and easier path to discovery. These customized algorithms, plug-ins, and workflow solutions can parse and analyze data exported from GenomeStudio software, Illumina's unified informatics solution.


Third-party tools are available for a broad range of genetic analysis applications including:

  • Sequence alignment, SNP calling, indel detection
  • Sequencing informatics workflow and data management
  • Whole-genome association
  • Copy number variation analysis
  • Gene expression analysis
  • eQTL analysis
  • Multi-assay data integration
  • Biological pathway and network analysis


SNP Genotyping & CNV Analysis Plug-Ins

Plug-in Source Functionality BeadStudio Module Compatibility GenomeStudio Module Compatibility Plug-in Type/
Download
CGHFusion Plug-in InfoQuant Export of GenomeStudio GT data in CGHFusion
N/A v2010.3+ Report / (ZIP)
ChromoZone Illumina Creates autobookmarks for single-sample analysis GT v3.0+ N/A Autobookmarking / (ZIP)
CNVPartition v1.2.1 Illumina Estimates copy number and annotates regions with copy number variants (CNV) GT v3.3.7+ N/A CNV / (ZIP)
CNVPartition v3.2.0 Illumina Estimates copy number and annotates regions with copy number variants (CNV) N/A GT v1.0+
CNV / (ZIP)
CNV Region Report
Illumina Generates i) A Standard Report that lists each copy number variation (CNV) and loss of heterozygosity (LOH) region for each sample; ii) An Allele-Specific Copy Number Report that reports copy number informed genotypes such as A- and ABB; iii) A PLINK CNV Input Report, which creates input files for some of the CNV features of the PLINK GWAS and CNV analysis application
N/A GT v1.0+
Report / (ZIP)
dChip InputReports Illumina Provides output data compatibility with dChip for CNV/LOH analysis GT v3.1+ (you must also have dChip installed) N/A Report / (ZIP)
Exemplar SapioSciences Provides output data compatibility with Exemplar for whole genome association studies (WGAS) GT v3.0+ N/A Report / (ZIP)
Haploview Input Report Plug-in v2.0.0 Illumina Export GT data for viewing in Haploview N/A GT v1.0+ Report / (ZIP)
Helix Tree DSF Golden Helix Provides output data compatibility with HelixTree for WGAS GT v3.0+ N.A Report / (ZIP)
Helix Tree DSF Report Golden Helix Export either genotype data or CNV data GT v3.1+ N/A Report / (ZIP), (PDF Readme)
Golden Helix GenomeStudio DSF Plug-in Golden Helix Provides output compatibility with SVS 7 for SNP and CNV analysis N/A GT v1.0+ Report / (ZIP)
(Doc Readme)
LOH Detector Illumina Detects extended tracts of homozygosity. GT v3.0+ N/A Autobookmarking / (ZIP)
LOH Score Illumina Estimates the likelihood of loss of heterozygostiy (LOH) in a region of interest. GT v3.0+ N/A Column / (ZIP)
Merlin Input Report Plug-in v1.0.1 Illumina Used to create input files for the Merlin application GT v3.2+ N/A Report / (ZIP)
Merlin Input Report Plug-in v2.0.1 Illumina Used to create input files for the Merlin application N/A GT v1.0+ Report / (ZIP)
Nexus Copy Number Plug-in BioDiscovery Export BeadStudio CNV data to Nexus Copy Number GT v3.1+ N/A Report / (ZIP)
Nexus Copy Number Plug-in BioDiscovery Export GenomeStudio CNV data to Nexus Copy Number N/A GT v1.0+ Report / (ZIP)
Partek Copy Number Report Plug-in
Partek Export copy number analysis data for use in Partek's Genomic Suite
N/A GT v.1.0+
Report / (ZIP)
PennCNV University of Pennsylvania Automated analysis and visualization of CNV calls GT v3.1+ via Universal CNV Adapter GT v1.0+ via Universal CNV Adapter CNV / (ZIP),
(HTML Tutorial)
PLINK Input Report Plug-in Illumina Allows you to create input files for PLINK N/A GT v1.0+ Report / (ZIP)
QuantiSNP Oxford University Automated analysis and visualization of CNV calls
GT v3.1+ via Universal CNV Adapter GT v1.0+ via Universal CNV Adapter CNV / Contact:
Ioannis Ragoussisor Cristopher Yau.
Universal CNV Adapter v1.0.4 Illumina Plug-in to QuantiSNP. For details, contact Illumina. GT v3.1+ N/A CNV / (ZIP)
Universal CNV Adapter v2.0.2 Illumina Plug-in to QuantiSNP. For details, contact Illumina. N/A GT v1.0+ CNV / (ZIP)

Gene Expression Analysis Plug-Ins

Plug-in Source Functionality BeadStudio Module Compatibility GenomeStudio Module Compatibility Plug-in Type/
Download
IBD 2.1 GenomStudio plug-in Integromics Integromics Biomarker Discovery™ (IBD) for TIBCO Spotfire® Custom Output Report for GenomeStudio™ Gene Expression Module N/A GX v1.0+ Report / (ZIP)
Illumina BeadStudio plugin for Nexus Expression BioDiscovery Export gene expression data for use in BioDiscovery's Nexus Expression GT v3.1+ N/A Report / (ZIP)
Illumina GenomeStudio plugin for Nexus Expression BioDiscovery Export gene expression data for use in BioDiscovery's Nexus Expression N/A GX v1.0+ Report / (ZIP)
ArrayExpress Data Submission Report v2.0.0 Illumina Export GX data in ArrayExpress format N/A GX v1.0+ Report / (ZIP)
GEO Data Submission Report Plug-in v1.0.0 Illumina Export GX module data in GEO format GX v3.2+ N/A Report / (ZIP)
GEO Data Submission Report Plug-in v2.0.0 Illumina Export GX module data in GEO format N/A GX v1.0+ Report / (ZIP)
GX Custom Output Report Plug-in v1.0.0 Illumina Used to configure several report parameters including output columns and sample display GX v3.3+ N/A Report / (ZIP)
GX Custom Output Report Plug-in v2.1.0 Illumina Used to configure several report parameters including output columns and sample display N/A GX v1.0+ Report / (ZIP)
Partek Gene Expression Report Plug-in
Partek Export gene expression data for use in Partek's Genomic Suite
N/A GT v.1.0+
Report / (ZIP)

Gene Regulation & Epigenetics Analysis Plug-Ins

Plug-in Source Functionality BeadStudio Module Compatibility GenomeStudio Module Compatibility Plug-in Type/
Download
Partek's Report Plug-In for GenomeStudio Partek Exports data into a project that Partek can directly open N/A GT v1.0+ Report / (ZIP)
Methylation Custom Output Report Plug-in v2.0.0 Illumina Used to create input files for downstream applications N/A GT v1.0+ Report / (ZIP)


For Research Use Only.