Informatics Infrastructure and Pipeline Setup
Discovery is possible when the right infrastructure is in place
Streamline your bioinformatics and data analysis pipeline so you can concentrate on the things that matter
Bioinformatics Infrastructure and Pipeline Considerations
What if the next big breakthrough has nothing to do with genomics but everything to do with the underlying bioinformatics pipeline you use to understand genomic data? At Illumina, we believe that the bioinformatics infrastructure you have set up—from the sequencer to the analysis tools you use—plays a critical role in your success.
The interdisciplinary nature of bioinformatics and genomics data analysis calls for a bioinformatics pipeline that promotes collaboration and reflects the way you can most efficiently and reliably process and analyze genomic data – now and into the future. Setting up a new next-generation sequencing (NGS) pipeline or simply adding components to an existing pipeline requires careful thought and planning.
Build or Buy Informatics Tools?
Labs often weigh considerations for purchasing bioinformatics tools from a reputable vendor against the advantages of in-house customization. The cost of developing do-it-yourself tools often exceeds the cost of purchasing tools, and commercial software developed with the user in mind tends to be easier for staff to use.
Many labs agree that if you can find a tool that meets most of your needs, has flexibility for customization, and is well supported, purchasing is a better use of resources. Learn more about the experiences of several labs who recently decided to purchase a LIMS.
Read Article: Four Main Reasons to Buy a LIMS
Benefits of Lab Automation
Introducing automation addresses several common challenges facing high-throughput genomic labs, such as ensuring consistency and reproducibility. A laboratory information management system (LIMS) provides:
- Sample tracking and standardized reporting
- Automated library prep
- Integration of instruments and liquid-handling robots into workflows
- End-to-end management of samples, tests, and results
Operationalize Informatics Workflows
Transform your bioinformatics operations with sequencing system integrations, scalable throughput, and an intuitive interface to select and customize your data analysis workflows. With Illumina Connected Analytics, data can be automatically analyzed with ready-to-use analysis pipelines or custom pipelines.
Learn More About Illumina Connected AnalyticsBioinformatics Pipeline Upgrades
Learn how upgrades to the Jackson Laboratory's data analysis pipeline have accelerated the lab's work, improving their ability to quickly understand large, complex genome and exome data sets.
Read ArticleSequencing Lab Automation
Explore solutions designed to meet the needs of production-scale sequencing labs, from automated library preparation to high-throughput sequencing instruments, high-volume data analysis and management, multiplexing, and more. Hear from scientists who have set up high-capacity sequencing labs. Learn more about:
High-Throughput SequencingLibrary Prep Automation
Microarray Lab Automation
We offer liquid-handling robots, array loaders, and other automation packages for labs conducting microarray-based genotyping and methylation studies. These packages help streamline the assay workflow and integrate sample preparation and array scanning. Learn more about:
High-Throughput GenotypingArray Automation Packages
A LIMS Tailored for Genomics Labs
Clarity LIMS is our laboratory information management system. Designed specifically for genomics labs and optimized for NGS, Clarity LIMS (formerly known as BaseSpace Clarity LIMS) integrates with instruments, helps labs track and manage samples, and streamlines the overall operations in a lab. In contrast to complicated homegrown systems, Clarity LIMS is designed with the end user in mind, encouraging wider adoption by lab staff.
View ProductData Sharing and Collaboration
Prepare your data for publication
Sequencing data has been traditionally difficult for non-bioinformatics experts to understand. Illumina solutions offer intuitive report formats that are tailored to biologists and are available in publication-ready formats.
Researchers can launch workflows with a click of a button and output user-friendly reports that can be easily shared with collaborators or public databases.
Collaborate
Sharing large sets of data can present obstacles involving arcane FTP protocols, hard drive limits, and incompatible device interfaces.
Illumina offers solutions such as Illumina Connected Analytics and BaseSpace Sequence Hub that make sharing data with trusted collaborators as simple as ever. With a click of a button, users can share individual sequencing runs or entire projects. Sharing is instantaneous and accessible everywhere.
Featured Solutions
Illumina Connected Analytics
A modular, secure data platform for scalable data management, analysis, and exploration. Generate insights with speed through shared datasets.
View Product
BaseSpace Sequence Hub
The Illumina cloud-based genomics computing environment for NGS data management and analysis. It fosters collaboration and innovation with simplified data sharing.
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Clarity LIMS
A LIMS that helps laboratories track samples and optimize workflows. Lab managers can access real-time data from mobile devices to update stakeholders or collaborators.
View ProductSample Management
Easily Manage Samples and Set Up Experiments
High-throughput genomics labs face the difficulty of managing/tracking samples and designing custom assays. We offer user-friendly tools to help start and manage your sequencing or microarray project.
Our informatics tools help you import biological sample information, design and pool libraries, prepare sequencing runs, create custom targeted sequencing panels, and generate sample sheets.
Sample Management for High-Throughput Labs
Modern genomics research generates an unprecedented amount of data. Faced with increasing data volumes and sample throughput, labs seeking to streamline lab operations and cut costs must modernize their approach.
A laboratory information management system (LIMS) is software that allows you to effectively manage samples and associated data. With this system, your lab can automate workflows and integrate with instruments to improve lab efficiency.
Learn More About LIMSSimple Sequencing Experiment Setup
Setting up and running sequencing experiments is easy with software designed for Illumina sequencing systems. The specific software tool to use depends on which Illumina sequencer is utilized.
Importance of Standards and QC
With rapidly advancing NGS technology, it’s critical to have quality control (QC) checks for the large volumes of data being generated. Illumina provides guidelines for using controls and standards in sequencing experiments, enabling researchers to maintain confidence in the quality of their data and experiment results.
- See what high-quality sequencing data should look like. View data examples
- Learn more about sequencing quality scores. Understand quality scores
- Learn more about PhiX, the standard control DNA used for Illumina sequencing experiments. View PhiX controls
Learn More
AI in Genomics
Explore how AI is accelerating sequence variant interpretation, enhancing variant calling accuracy, and enabling multiomic discovery across research workflows.
Sequencing Data Analysis
User-friendly tools smooth the process of analyzing sequencing data, so you can spend more time doing research and less time configuring workflows.
Choosing a LIMS for NGS
Find out what features to look for when selecting a LIMS for NGS. Learn how instrument integration and NGS-specific features aid implementation.