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


Illumina Connect Partners

GenomeStudio Plug-Ins

SNP Genotyping & CNV Analysis Plug-Ins

Plug-inSourceFunctionalityBeadStudio Module CompatibilityGenomeStudio Module CompatibilityPlug-in Type/
Download
CGHFusion Plug-in InfoQuant Export of BeadStudio GT data into CGHFusion GT v3.2+ N/A 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 v2.4.4 Illumina Estimates copy number and annotates regions with copy number variants (CNV) N/A GT v1.0 & KaryoStudio 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)
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 v2.1.1 Illumina Used to create input files for the Merlin application N/A GT v1.0+ Report / (ZIP)
Nexus CGH Report Plug-in BioDiscovery Export BeadStudio CNV data to Nexus CGH GT v3.1+ N/A Report / (ZIP)
Nexus Copy Number Plug-in for CNV Analysis 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 v2.1.3 Illumina Plug-in to QuantiSNP. For details, contact Illumina. N/A GT v1.0+ CNV / (ZIP)

Gene Expression Analysis Plug-Ins

Plug-inSourceFunctionalityBeadStudio Module CompatibilityGenomeStudio Module CompatibilityPlug-in Type/
Download
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-inSourceFunctionalityBeadStudio Module CompatibilityGenomeStudio Module CompatibilityPlug-in Type/
Download
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 ApplicationLIMS / Data Management
Illumina iConnect PartnerPartner TypeDNA/RNA SequencingGenotyping / CNVGene ExpressionSequencingMicroarrayPlug-in Available
Ariadne Genomics Commercial
Ariadne Genomics

9430 Key West Avenue
Rockville, MD 20850

Software: Pathway Studio
Contact: David Denny
Phone: 1.240.453.6272
Email: ddenny@ariadnegenomics.com
Web: www.ariadnegenomics.com
BioBase Commercial
BioBase

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
BioComputing Platforms Commercial
BioComputing Platforms Ltd.

Innopoli 2
Tekniikantie 14
02150 Espoo
Finland

Software: BC|Gene, BC|SNP
Contact: Anni Ahonen-Bishopp
Phone: +358.40.5780587
Email: anni.ahonen-bishopp@bcplatforms.com
Web: www.bcplatforms.com
BioDiscovery Inc Commercial
BioDiscovery

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
BioTeam, Inc.

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
CLC bio

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
dChip

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
DNASTAR Inc.

3801 Regent Street
Madison, WI 53705 USA

Software: Variant Detection (Lasergene), RNASeq and DGE (QSeq), Mapping/Annotation (NGen), Assembly (using NGen)
Contact: Bob Steinhauser
Phone: 1.608.258.7420
Email: steinhauserb@dnastar.com
Web: www.dnastar.com
GeneData Commercial
Genedata AG

Maulbeerstrasse 46
CH-4016 Basel, Switzerland

Software: Expresssionist
Contact: Mikaela Gabrielli
Phone: +41 61 511 8429
Email: expressionist@genedata.com
Web: www.genedata.com
GeneGo Commercial
GeneGo

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
Genomatix Commercial
Genomatix Software, Inc.

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
GenomeQuest

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
Geospiza Commercial
Geospiza, Inc.

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
GLS Genologics Commercial
GenoLogics Life Sciences Software

4464 Markham Street, Suite 2302
Victoria, BC, Canada, V8Z 7X8

LIMS: Geneus
Contact: Laurie Phillips
Phone: 1.866.457.5467, 1.250.483.7011
Email: laurie.phillips@genologics.com
Web: www.genologics.com
Golden Helix Commercial
Golden Helix, Inc.

716 S. 20th Ave., Suite 102
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
GraphLogic Inc.

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
infoQuant

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
InforSense, LLC

155 Second Street
Cambridge, MA 02141

Contact: Robin Munro
Phone: +44 20 8237 8453
Email: rmunro@inforsense.com
Web: www.inforsense.com
Ingenuity Commercial
Ingenuity Systems, Inc.

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
LUMI Academic
LUMI

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
Partek Incorporated

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
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
Progeny Commercial
Progeny Software, LLC

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
Sapio Sciences, LLC

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 Institute Inc.

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
Synamatix

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
University of Pennsylvania

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
The Wellcome Trust Centre for Human Genetics

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