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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

Illumina Connect Partners GenomeStudio Plug-Ins

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 Connect Partner
Partner Type
DNA/RNA Sequencing
Genotyping / CNV
Gene Expression
Sequencing
Microarray
Plug-in Available
BioBase
Commercial
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
BC Platforms
Commercial
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
BioDiscovery Inc
Commercial
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
The BioTeam
Commercial
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
CLC bio
Commercial
Gustav Wieds Vej 10
8000 Aarhus C
Denmark

Software: CLC Genomics Workbench
Contact: Thomas Knudsen
Email: tknudsen@clcbio.com
Web: www.clcbio.com
dChip
Academic

Analysis and visualization of gene expression and SNP microarrays

Harvard School of Public Health and Department of Biostatistics and Computational Biology
Dana-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
DNAStar
Commercial
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
Genedata
Commercial
Margarethenstrasse 38
CH-4053, Basel, Switzerland

Software: Expresssionist
Contact: Silke Oeschger
Phone: +41 61 511 84 561
Email: expressionist@genedata.com
Web: www.genedata.com
GeneGo
Commercial
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
GenoLogics
Commercial
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
Genomatix
Commercial
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
GenomeQuest
Commercial
700 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
Geospiza
Commercial
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
Golden Helix
Commercial
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
GraphLogic
Commercial
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
InfoQuant
Commercial
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
InforSense
Commercial
155 Second Street
Cambridge, MA 02141

Contact: Robin Munro
Phone: +44 20 8237 8453
Email: rmunro@inforsense.com
Web: www.inforsense.com
Ingenuity
Commercial
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
Intrepid Bioinformatics
Commercial
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
LUMI
Academic

An integrated solution for Illumina microarray data analysis, available as an R/Bioconductor application.

Robert H. Lurie Comprehensive Cancer Center
676 N Saint Clair, Suite 1200
Northwestern University
Chicago, IL 60611

Contact: Dr Simon Lin
Email: s-lin2@northwestern.edu
Web: www.bioconductor.org
Partek
Commercial
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
PLINK
Academic

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
Progeny
Commercial
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
Sapio
Commercial
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
SAS/JMP Genomics
Commercial
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
Synamatix
Commercial
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
University of Pennsylvania
Academic
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
The Wellcome Trust Centre for Human Genetics
Academic
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

For Research Use Only.