System Literature
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HiSeq Applications BrochureBrochure | PDF | 4 MB
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HiSeq Sequencing SystemsBrochure | PDF | 2 MB
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Illumina Sequencing Platforms BrochureBrochure | PDF | < 1 MB
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TruSeq v3 Advancements for HiSeq SystemsBrochure | PDF | 1 MB
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A Patient-Centric SNV-CNV PipelineTechnical Note | PDF | < 1 MB
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Configuring Virus Scanner Software on Illumina SequencersTechnical Note | PDF | < 1 MB
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DNA-Seq Data ProcessingTechnical Note | PDF | < 1 MB
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Data Analysis: GWAS ProcessingTechnical Note | PDF | < 1 MB
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Data Analysis: Microarray Gene ExpressionTechnical Note | PDF | < 1 MB
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Data Correlation Details: Enrichment AnalysisTechnical Note | PDF | < 1 MB
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Estimating Sequencing CoverageTechnical Note | PDF | < 1 MB
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Low-Diversity Sequencing on the Illumina HiSeq PlatformsTechnical Note | PDF | < 1 MB
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Meta-Analysis FrameworkTechnical Note | PDF | < 1 MB
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RNA-Seq Data ProcessingTechnical Note | PDF | < 1 MB
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Using a PhiX Control for HiSeq Sequencing RunsTechnical Note | PDF | < 1 MB
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Reducing Whole-Genome Data Storage FootprintWhite Paper | PDF | < 1 MB
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Cost-Effective Sequencing Enables Researchers to Scale Cancer Studycase_study | PDF | < 1 MB
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HiSeq 1500/2500 Specification Sheet,HiSeq 2500 Sequencing SystemData Sheet | PDF | < 1 MB
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HiSeq 2500 Sequencing SystemData Sheet | PDF | < 1 MB
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Using Large Sample Sizes and Deep Sequencing to Find the Root Cause for Psychiatric Disordersicommunity_articles | PDF | < 1 MB
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RNA-Seq Studies Identify Biomarkers for Early Detection of Pulmonary Diseasesicommunity_articles | PDF | < 1 MB
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Illumina Sequencing Portfolio Brochure,Sequencing Systems PortfolioBrochure | PDF | 9 MB
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Illumina Security Best Practices GuideTechnical Note | PDF | < 1 MB
Product Selection and Experiment Planning Tools
Find tools to help you choose the right products for your needs and plan your experiments. Identify the right library prep kit or microarray, calculate sequencing coverage, explore methods compiled from publications, design custom assays, and more.
Explore Tools
Education and Support Resources
HiSeq 2500 System Guide
Provides an overview of instrument components and instructions for operating and maintaining the HiSeq 2500.
HiSeq Site Prep Guide
Lab specifications and requirements for preparing the lab for sequencing on the HiSeq 2500 System.
Sequencing Online Training
Online Illumina sequencing courses are free, interactive, and available any time.
Personalized Training Workflow Selection Tool
This tool will help you determine the best hands-on sequencing training for your needs based on your area of interest, application, library preparation kit, and platform.
Sequencing Coverage
Sequencing coverage describes the average number of NGS reads that align to known reference bases. Coverage requirements vary by application.
Quality Scores
Additional information about sequencing quality scores, how they are calculated, and the relationship between quality score and base call accuracy.
HiSeq 2500 Documentation
Support resources including guides, upgrade resources, and the latest support updates for the HiSeq 2500.
Sequencing Troubleshooting Tips
These short videos provide expert tips for common sequencing issues such as overclustering and inconsistent quantitation.
Custom Protocol Selector
The Custom Protocol Selector enables you to generate your own customized documentation, specifically tailored to your experiment.
The HiSeq 2500 System has been obsolesced. We intend to continue to provide full support of the instrument and supply the reagents through February 28th, 2023. We also offer several instruments that support the same applications as the HiSeq 2500 System; we recommend using the Sequencing Platform Comparison Tool to find the best instrument for your needs.
Customer Stories
Progress in Rapid Identification of Variants Linked to Genetic Diseases
Learn how DNA sequencing is leading to progress in the rapid identification of variants that might be involved in genetic diseases. Thanks to this work, Dr. Kingsmore and his team now hold a Guinness World Records title.
View VideoExploring the Genetic Basis of Oral Cancer
Researchers in India study a deadly oral cancer that is strongly associated with chewing tobacco together with slaked lime.
Read ArticleNGS Identifies Rare Disease Variants in Infants with Undiagnosed Disease
Landmark NGS study leads to a national clinical diagnostic exome sequencing platform in Singapore.
Read ArticleVideos and Webinars
Toward Precision Medicine in Neuropsychiatry
David Goldstein at the Center for Human Genome Variation shares how sequencing with the HiSeq 2500 helps advance neuropsychiatry.
Attack of the Jet-Lagged Tomatoes
Learn how tomato circadian clocks and genes evolved as tomatoes were transferred from their equatorial birthplace and planted across North America.
Gut-Brain Axis: Melancholy of Our Gut Microbiome
Learn how transplanting gut microbes from patients diagnosed with depression affects the mental state of germ-free mice.