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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:
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- 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
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Ariadne Genomics
9430 Key West Avenue
Rockville, MD 20850
Phone: 240.453.6272
Contact: David Denny
Email: ddenny@ariadnegenomics.com
Web: www.ariadnegenomics.com
Application Area Supported: Gene Expression (GEX)
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BioBase
BIOBASE GmbH Halchtersche Strasse 33
D-38304 Wolfenbuettel/Germany
Phone: +49.53.31.8584 0
Contact: Frank Schacherer
Email: Frank.Schacherer@biobase-international.com
Web: www.biobase-international.com
Application Area Supported: Gene Expression Analysis
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BioComputing Platforms Ltd.
Innopoli 2
Tekniikantie 14
02150 Espoo
Finland
Phone: +358.40.5780587
Contact: Anni Ahonen-Bishopp
Email: anni.ahonen-bishopp@bcplatforms.com
Web: www.bcplatforms.com
Application Area Supported: Genotyping (GT)
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BioDiscovery
2121 Rosecrans Ave., Suite 3315
El Segundo, CA 90245
Phone: 310.414.8100
Contact: Dr Soheil Shams
Email: sshams@biodiscovery.com
Web: www.biodiscovery.com
Application Areas supported: Genotyping (GT), Copy Number (CN) analysis
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BioTeam, Inc.
7 Derosier Drive
Middleton, MA 01949
Phone: 877.246.2992 x101
Contact: Stan Gloss
Email: stan@bioteam.net
Web: www.bioteam.net/specialty/nextGenSeq.html
Application Areas supported: WIKI-LIMS for Sequencing applications
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CLC bio
Gustav Wieds Vej 10
8000 Aarhus C
Denmark
Contact: Thomas Knudsen
Email: tknudsen@clcbio.com
Web: http://www.clcbio.com/ngs
Application Area Supported: Sequencing Solutions
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DNASTAR Inc.
3801 Regent Street
Madison, WI 53705 USA
Phone: 608.258.7420
Contact: Bob Steinhauser
Email: steinhauserb@dnastar.com
Web: http://www.dnastar.com
Application Areas supported: Gene Expression & Sequencing
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Genedata AG
Maulbeerstrasse 46
CH-4016 Basel, Switzerland
Phone: +41 61 511 8429
Contact: Mikaela Gabrielli
Email: expressionist@genedata.com
Web: www.genedata.com
Application Area Supported: Gene Expression (GEX)
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GeneGo
169 Saxony Rd, Suite 109
Encinitas, CA 92024
Phone: 858.756.7996
Contact: Julie Bryant
Email: julie@genego.com
Web: www.genego.com/metacore.php
Application Area Supported: Pathway Analysis & Gene Expression
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GenoLogics Life Sciences Software
4464 Markham Street, Suite 2302
Victoria, BC, Canada, V8Z 7X8
Phone: 1.866.457.5467, 1.250.483.7011
Contact: Laurie Phillips
Email: laurie.phillips@genologics.com
Web: www.genologics.com
Application Areas Supported: Genotyping (GT), Copy Number Variation Analysis (CNV), Methylation Profiling, Gene Expression (GEX), and Sequencing
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GenomeQuest
1700 West Park Drive, Suite 260
Westborough, MA 01581
Phone: 508.616.0100 x121
Contact: Anthony Salerno
Email: anthony.salerno@genomequest.com
Web: www.genomequest.com
Application Areas Supported: Sequencing applications
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Geospiza, Inc.
100 West Harrison
Seattle, WA 98119
Phone: 206.633.4415
Contact: Laura Lucas
Contact phone: 206.633.4403 x 119
Email: laural@geospiza.com
Web: http://www.geospiza.com
Application Area Supported: Whole-Genome SNP Analysis, Copy Number Variation (CNV) Analysis, Gene Expression Analysis, Sequencing Application
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Golden Helix, Inc.
716 S. 20th Ave., Suite 102
Bozeman, MT 59718
Phone: 406.585.8137
Contact: Josh L. Forsythe
Email: jlforsythe@goldenhelix.com
Web: www.goldenhelix.com
Application Area Supported: Genotyping (GT), Copy Number (CN) analysis
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GraphLogic Inc.
388 E. Main Street
Branford CT 06405
Phone: 203.488.1922 x105
Fax: 203.488.1802
Contact: Julie Pellegrini
Email: jpellegrini@graphlogic.com
Web: www.graphlogic.com
Application Area Supported: Sequencing – LIMS
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infoQuant
Suite 326
8 Shepherd Market
London W1J 7JY, UK
Phone: 617.475.5167
Contact: Anton Petrov
Email: info@infoquant.com
Web: www.infoquant.com
Application Area Supported: Copy Number (CN) analysis
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InforSense, LLC
155 Second Street
Cambridge, MA 02141
Phone: +44 20 8237 8453
Contact: Robin Munro
Email: rmunro@inforsense.com
Web: www.inforsense.com
Application Area Supported: Genotyping (GT)
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Ingenuity Systems, Inc.
1700 Seaport Blvd. Suite 300
Redwood City, CA 94063
Phone: 650.381.5150
Contact: Heidi Bullock
Email: hbullock@ingenuity.com
Web: www.ingenuity.com
Application Area Supported: Gene Expression (GEX)
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Partek Incorporated
12747 Olive Blvd., Suite 205
St. Louis, Missouri 63141
Phone: 314.878.2329
Contact: Shirley Gross
Email: sgross@partek.com
Web: www.partek.com
Application Areas Supported: Genotyping (GT), Gene Expression (GEX), Copy Number Variation Analysis (CNV)
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Progeny Software, LLC
130 S. Main Street, Suite 120
South Bend, IN 46601
Phone: 800.776.4369
Contact: Andrew Brown, Ph.D.
Email: abrown@progenygenetics.com
Web: www.progenygenetics.com
Application Area Supported: Genotyping (GT)
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Rosetta BioSoftware
401 Terry Ave. N.
Seattle, WA 98109
Phone: 206.926.1200
Contact: Carol Preisig
Email: preisig@rosettabio.com
Web: Visit Resolver site
Web: Visit Syllego site
Application Areas Supported: Genotyping(GT), Copy Number Variation (CNV), Gene Expression (GEX).
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Sapio Sciences, LLC
2391 Mayfield Street, Suite 201
York, PA 17402
Phone: 301.576.2729
Contact: Dr Kevin Cramer
Email: kcramer@sapiosciences.com
Web: www.sapiosciences.com
Application Areas Supported: Copy Number (CN) analysis, Genotyping (GT)
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SAS Institute Inc.
SAS Campus Drive
Cary, North Carolina 27513
Phone: 919.677.8008
Contact: Doug Robinson, Ph.D.
Email: Doug.Robinson@jmp.com
Web: www.jmp.com
Application Areas Supported: Genotyping (GT), Gene Expression (GEX)
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Stratagene, Inc.
11011 N. Torrey Pines Road
La Jolla, CA 92037
Phone: 858.373.6300
Contact: Dr David Edwards
Email: david.edwards@stratagene.com
Web: www.stratagene.com
Application Areas Supported: Copy Number (CN) analysis, Gene Expression (GEX)
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Synamatix
27-9, Level 9, Signature Office
Bandar Mid-Valley
59200 Kuala Lumpur
Malaysia
Phone: +6012 2607333
Contact: Arif Anwar, Ph.D.
Email: arifanwar@synamatix.com
Web: www.synamatix.com
Application Areas Supported: Sequencing informatics
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VizX Labs/GeneSifter
Queen Anne Square
200 West Mercer St., Suite 500
Seattle, WA 98119-3995
Phone: 877.932.4363
Contact: Jeff Kozlowski
Email: jeff@genesifter.net
Web: www.genesifter.net
Application Area Supported: Gene Expression (GEX)
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illumina•Connect academic partners
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University of Pennsylvania
Department of Genetics
University of Pennsylvania
Philadelphia, PA 19104
Phone: 215.898.0021
Contact: Kai Wang
Email: kai@mail.med.upenn.edu
Web: www.neurogenome.org/cnv/penncnv/
Application Areas Supported: Copy Number Variation Analysis (CNV)
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The Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford
OX3 7BN
United Kingdom
Phone: +44 (0)1865 287500
Contact: Iaonnis Ragoussis
Email: ioannisr@well.ox.ac.uk
Web: www.well.ox.ac.uk
Application Area Supported: Copy Number Variation (CNV) analysis
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plink...
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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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dChip
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dChip
Analysis and visualization of gene expression and SNP microarrays
Contact: Dr Cheng Li
Department of Biostatistics, Harvard School of Public Health and
Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute
375 Longwood Ave, 6th Floor
Boston, MA, 02215
Email: cli@hsph.harvard.edu
Web: http://biosun1.harvard.edu/complab/dchip/
Application Areas Supported: Copy Number Variation (CNV) analysis, Gene Expression (GEX)
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LUMI
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LUMI
An integrated solution for Illumina microarray data analysis, available as an R/Bioconductor application.
Contact: Dr Simon Lin
Robert H. Lurie Comprehensive Cancer Center
676 N Saint Clair, Suite 1200
Northwestern University
Chicago, IL 60611
Email: S-Lin2@northwestern.edu
Web: http://www.bioconductor.org/packages/2.0/bioc/html/lumi.html
Application Area Supported: Gene Expression (GEX)
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GenomeStudio and BeadStudio plug-ins available from Illumina and third parties
 CNV Analysis Plug-ins
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Name |
Source |
Functionality |
BeadStudio Module Compatibility |
GenomeStudio Module Compatibility |
*.zip file
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cnvPartition v1.2.1 |
Illumina |
Estimates copy number and annotates regions with copy number variants (CNV) |
GT v3.3.7 |
N/A |
*.zip file
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cnvPartition v2.3.4 |
Illumina |
Estimates copy number and annotates regions with copy number variants (CNV) |
N/A |
GT v1.0
(also works with KaryoStudio)
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*.zip file
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ChromoZone |
Illumina |
Creates autobookmarks for single-sample analysis |
GT v3.0 and higher |
N/A |
*.zip file
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dChip InputReports |
Illumina |
Provides output data compatibility with dChip for CNV/LOH analysis |
GT v3.1 and higher
You must also have dChip installed |
N/A |
*.zip file
Read Me |
Helix Tree Dsf Report |
Golden Helix |
Export either
genotype data or CNV data |
GT v3.1 and higher |
N/A |
*.zip file
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Nexus CGH Plug-in for CNV Analysis |
BioDiscovery |
Export Illumina CNV data to Nexus CGH |
GT v3.1 and higher |
N/A |
*.zip file
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Partek GS custom report for CNV analysis |
Partek |
Export genotyping or CNV data to Partek GS |
GT v 3.1 and higher |
N/A |
*.zip file
Tutorial |
PennCNV |
U of Pennsylvania |
Automated analysis and visualization of CNV calls |
GT v3.1 and higher via Universal CNV Adapter |
GT v1.0 and higher via Universal CNV Adapter |
| Contact: Ioannis Ragoussis or Christopher Yau. |
QuantiSNP |
Oxford U |
For details, contact Ioannis Ragoussis or Christopher Yau |
GT v3.1 and higher via Universal CNV Adapter |
GT v1.0 and higher via Universal CNV Adapter |
*.zip file
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Universal CNV Adapter v1.0.4
(compatible with QuantiSNP & PennCNV)
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Illumina |
Plug-in to QuantiSNP. For details, contact Illumina. |
GT v3.1 and higher |
N/A |
*.zip file
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Universal CNV Adapter v2.0.2
(compatible with QuantiSNP & PennCNV)
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Illumina |
Plug-in to QuantiSNP. For details, contact Illumina. |
N/A |
GX v1.0 and higher |
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Learn more about analyzing CNV with Illumina BeadStudio plug-ins.
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LOH Analysis Plug-ins
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| Download |
Name |
Source |
Functionality |
BeadStudio Module Compatibility |
GenomeStudio Module Compatibility |
*.zip file
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LOH Detector |
Illumina |
Detects extended tracts of homozygosity |
GT v3.0 and higher |
N/A |
*.zip file
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LOH Score |
Illumina |
Estimates the likelihood of loss of heterozygostiy (LOH) in a region of interest |
GT v3.0 and higher |
N/A |
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Custom Report Plug-ins
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| Download |
Name |
Source |
Functionality |
BeadStudio Module Compatibility |
GenomeStudio Module Compatibility |
*.zip file
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CGHFusion Plugin |
InfoQuant |
Export of BeadStudio GT data into CGHFusion |
GT v3.2 and higher |
N/A |
*.zip file
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ArrayAssist Explorer v1 from Strand |
Stratagene / Agilent |
Provides output data from BeadStudio to ArrayAssist |
GX v3.2 and higher |
N/A |
*.zip file
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ArrayExpress Data Submission Report Plug-in v1.0.0 |
Illumina |
Export GX data in ArrayExpress format |
GX v3.2 and higher |
N/A |
*.zip file
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ArrayExpress Data Submission Report Plug-in v2.0.0 |
Illumina |
Export GX data in ArrayExpress format |
N/A |
GX v1.0 and higher |
*.zip file
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Exemplar |
Sapio Sciences |
Provides output data compatibility with Exemplar for whole genome association studies (WGAS) |
GT v3.0 and higher |
N/A |
*.zip file
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GEO Data Submission Report Plug-in v1.0.0 |
Illumina |
Export GX module data in GEO format |
GX v3.2 and higher |
N/A |
*.zip file
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GEO Data Submission Report Plug-in v2.0.0 |
Illumina |
Export GX module data in GEO format |
N/A |
GX v1.0 and higher |
*.zip file
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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 and higher |
N/A |
*.zip file
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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 and higher |
*.zip file
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HelixTree DSF |
Golden Helix |
Provides output data compatibility with HelixTree for WGAS |
GT v3.0 and higher |
N/A |
*.zip file
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Haploview Input Report Plug-in v2.0.0 |
Illumina |
Export GT data for viewing in Haploview |
N/A |
GT v1.0 and higher |
*.zip file
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Merlin Input Report Plug-in |
Illumina |
Used to create input files for the Merlin application |
GT v3.2 and higher |
N/A |
*.zip file
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Merlin Input Report Plug-in |
Illumina |
Used to create input files for the Merlin application |
N/A |
GT v1.0 and higher |
*.zip file
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Methylation Custom Output Report Plug-in v2.0.0 |
Illumina |
Used to create input files for downstream applications |
N/A |
GT v1.0 and higher |
*.zip file
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PLINK Input Report Plug-in v2.1.0 |
Illumina |
Allows you to create input files for PLINK |
N/A |
GT v1.0 and higher |
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BeadStudio software is transitioning to GenomeStudio software, Illumina’s complete informatics solution for analysis of sequencing- and array-based data. BeadStudio users with an active iScan System, BeadArray, or BeadXpress Reader warranty are eligible for a free upgrade to GenomeStudio software.
The GenomeStudio software installer and associated documents are available on iCom.
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overview
genome analyzer
humanomni1-quad
