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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
Illumina Connect
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 Ragoussis or 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) |
| Product Type | ||||||||
|---|---|---|---|---|---|---|---|---|
| Software Application | LIMS / Data Management | |||||||
| Illumina iConnect Partner | Partner Type | DNA/RNA Sequencing | Genotyping / CNV | Gene Expression | Sequencing | Microarray | Plug-in Available | |
| BioBase | Commercial |  |
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 BIOBASE GmbH Halchtersche Strasse 33 D-38304 Wolfenbuettel/Germany Software: ExPlain, BKL Contact: Frank Schacherer Phone: +49.53.31.8584 0 Email: Frank.Schacherer@biobase-international.com Web: www.biobase-international.com |
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| BC Platforms | Commercial | |
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 Innopoli 2 Tekniikantie 14 02150 Espoo Finland Software: BC/SNPmax, BC/GENE, BC/CLIN, BC/SAMPLE, BC/SEQUENCE, BC/CNV, BC/MultiQTL Contact: Paul Watkins Phone: +358 9 2517 7340 (EU) 858 215 1071 (USA) Email: paul.watkins@bcplatforms.com Web: www.bcplatforms.com |
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| BioDiscovery Inc | Commercial | |
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 2121 Rosecrans Ave., Suite 3315 El Segundo, CA 90245 Software: Nexus Expression, Nexus Copy Number Contact: Dr. Soheil Shams Email: sshams@biodiscovery.com Contact: Raja Keshavan Email: raja@biodiscovery.com Phone: 310.414.8100 Web: www.biodiscovery.com |
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| The BioTeam | Commercial | |
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 7 Derosier Drive Middleton, MA 01949 LIMS: WikiLIMS Contact: Stan Gloss Phone: 1.877.246.2992 x101 Email: stan@bioteam.net Web: www.bioteam.net |
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| CLC bio | Commercial | |
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 Gustav Wieds Vej 10 8000 Aarhus C Denmark Software: CLC Genomics Workbench Contact: Thomas Knudsen Email: tknudsen@clcbio.com Web: www.clcbio.com |
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| dChip | Academic | |
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dChip
Analysis and visualization of gene expression and SNP microarrays Harvard School of Public Health and Department of Biostatistics and Computational BiologyDana-Farber Cancer Institute 375 Longwood Ave, 6th Floor Boston, MA, 02215 Contact: Dr Cheng Li Phone: +44 (0)1865 287500 Email: cli@hsph.harvard.edu Web: biosun1.harvard.edu |
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| DNAStar | Commercial | |
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 3801 Regent Street Madison, WI 53705 USA Software: Lasergene Genomics Suite Contact: Tom Schwei Phone: 1.608.237.3082 Email: toms@dnastar.com Web: www.dnastar.com |
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| Genedata | Commercial | |
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 Margarethenstrasse 38 CH-4053, Basel, Switzerland Software: Expresssionist Contact: Kerstin Fink Phone: +41 61 511 8433 Email: expressionist@genedata.com Web: www.genedata.com |
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| GeneGo | Commercial | |
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 169 Saxony Rd, Suite 109 Encinitas, CA 92024 Software: MetaCore Contact: Julie Bryant Phone: 1.858.756.7996 Email: julie@genego.com Web: www.genego.com |
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| GenoLogics | Commercial | |
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 4464 Markham Street, Suite 2320 Victoria, BC, Canada, V8Z 7X8 LIMS: GenoLogics LIMS Products: GenoLogics LIMS & GenoLogics LIMS Preconfigured Package for Illumina NGS Contact: Sales Phone: 1.866.457.5467, 1.250.483.7011 Email: info@genologics.com Web: www.genologics.com |
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| Genomatix | Commercial | |
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 3025 Boardwalk, Suite 160 Ann Arbor, MI 48108 Contact: Peter Grant Phone: 1.877.436.6628 Email: grant@genomatix-software.com Web: www.genomatix-software.com |
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| GenomeQuest | Commercial | |
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 1700 West Park Drive, Suite 260 Westborough, MA 01581 Software: GenomeQuest 6.0 Contact: Anthony Salerno Phone: 1.508.616.0100 x121 Email: anthony.salerno@genomequest.com Web: www.genomequest.com |
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| Geospiza | Commercial | |
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 100 West Harrison Seattle, WA 98119 Software: GeneSifter, Clould based NGS Analysis Contact: Laura Lucas Contact Phone: 1.206.633.4403 x 119 Phone: 1.206.633.4415 Email: laural@geospiza.com Web: www.geospiza.com |
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| Golden Helix | Commercial | |
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 203 Enterprise Blvd., Suite 1 Bozeman, MT 59718 Software: SNP and Variation Suite Contact: Josh L. Forsythe Phone: 1.406.585.8137 Email: jlforsythe@goldenhelix.com Web: www.goldenhelix.com |
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| GraphLogic | Commercial | |
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 388 E. Main Street Branford CT 06405 Software: GEX analysis LIMS: Sequencing LIMS Contact: Julie Pellegrini Phone: 1.203.488.1922 x105 Fax: 1.203.488.1802 Email: jpellegrini@graphlogic.com Web: www.graphlogic.com |
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| InfoQuant | Commercial | |
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 8 Shepherd Market, Suite 326 London W1J 7JY, UK Software: CGHFusion Contact: Anton Petrov Phone: 1.617.475.5167 Email: info@infoquant.com Web: www.infoquant.com |
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| InforSense | Commercial | |
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 155 Second Street Cambridge, MA 02141 Contact: Robin Munro Phone: +44 20 8237 8453 Email: rmunro@inforsense.com Web: www.inforsense.com |
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| Ingenuity | Commercial | |
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 1700 Seaport Blvd. Suite 300 Redwood City, CA 94063 Software: Ingenuity Pathway Analysis Contact: Heidi Bullock Phone: 1.650.381.5150 Email: hbullock@ingenuity.com Web: www.ingenuity.com |
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| Intrepid Bioinformatics | Commercial | |
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 201 E. Jefferson Street, Suite 125 Louisville, KY 40202 Contact: Ted Kalbfleisch Phone: 1.502.212.2699 Email: ted@intrepidbio.com Web: www.intrepidbio.com |
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| LUMI | Academic | |
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LUMI
An integrated solution for Illumina microarray data analysis, available as an R/Bioconductor application. Robert H. Lurie Comprehensive Cancer Center676 N Saint Clair, Suite 1200 Northwestern University Chicago, IL 60611 Contact: Dr Simon Lin Email: s-lin2@northwestern.edu Web: www.bioconductor.org |
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| Partek | Commercial | |
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 12747 Olive Blvd., Suite 205 St. Louis, Missouri 63141 Software: Partek Genomics Suite Contact: Shirley Gross Email: sgross@partek.com Contact: Tom Downey Email: tjd@partek.com Contact: Mike Lelivelt Email: mlelivelt@partek.com Phone: 1.314.878.2329 Web: www.partek.com |
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| PLINK | Academic | |||||||
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PLINK
Whole genome association analysis toolset. The link below describes how Illumina’s WG arrays data from BeadStudio can be converted into a file input format for WGAS using PLINK. PLINK Support for BeadStudio data output |
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| Progeny | Commercial | |
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 130 S. Main Street, Suite 120 South Bend, IN 46601 Software: Progeny LAB LIMS: Progeny LIMS Contact: Andrew Brown, Ph.D. Phone: 1.800.776.4369 Email: abrown@progenygenetics.com Web: www.progenygenetics.com |
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| Sapio | Commercial | |
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 2391 Mayfield Street, Suite 201 York, PA 17402 Software: Exemplar Analytics LIMS: Exemplar LIMS Contact: Dr. Kevin Cramer Phone: 1.301.576.2729 Email: kcramer@sapiosciences.com Web: www.sapiosciences.com |
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| SAS/JMP Genomics | Commercial | |
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 SAS Campus Drive Cary, North Carolina 27513 Software: JMP Genomics Contact: Doug Robinson, Ph.D. Phone: 1.919.677.8008 Email: doug.robinson@jmp.com Web: www.jmp.com |
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| Synamatix | Commercial | |
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 27-9, Level 9, Signature Office Bandar Mid-Valley 59200 Kuala Lumpur, Malaysia Software: SynaBASE Contact: Arif Anwar, Ph.D. Phone: +6012 2607333 Email: arifanwar@synamatix.com Web: www.synamatix.com |
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| University of Pennsylvania | Academic | |
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 Department of Genetics University of Pennsylvania Philadelphia, PA 19104 Contact: Kai Wang Phone: 1.215.898.0021 Email: kai@mail.med.upenn.edu Web: www.neurogenome.org |
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| The Wellcome Trust Centre for Human Genetics | Academic | |
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 Roosevelt Drive Oxford OX3 7BN United Kingdom Contact: Iaonnis Ragoussis Phone: +44 (0)1865 287500 Email: ioannisr@well.ox.ac.uk Web: www.well.ox.ac.uk |
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Innovative technologies
At Illumina, our goal is to apply innovative technologies and revolutionary assays to the analysis of genetic variation and function, making studies possible that were not even imaginable just a few years ago. These studies will help make the realization of personalized medicine possible. With such rapid advances in technology taking place, it is mission critical to have solutions that are not only innovative, but flexible, scalable, and complete with industry-leading support and service. As a global company that places high value on collaborative interactions, rapid delivery of solutions, and prioritizing the needs of its customers, we strive to meet this challenge. Illumina's innovative, array-based solutions for DNA, RNA, and protein analysis serve as tools for disease research, drug development, and the development of molecular tests in the clinic.
At Illumina, our goal is to apply innovative technologies and revolutionary assays to the analysis of genetic variation and function, making studies possible that were not even imaginable just a few years ago. These studies will help make the realization of personalized medicine possible. With such rapid advances in technology taking place, it is mission critical to have solutions that are not only innovative, but flexible, scalable, and complete with industry-leading support and service. As a global company that places high value on collaborative interactions, rapid delivery of solutions, and prioritizing the needs of its customers, we strive to meet this challenge. Illumina's innovative, array-based solutions for DNA, RNA, and protein analysis serve as tools for disease research, drug development, and the development of molecular tests in the clinic.
© 2012 Illumina, Inc. All rights reserved.