Skip to content

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 a do-it-yourself system often exceeds the cost of purchasing a LIMS, 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 LIMS 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 made this decision.

Read Article

Benefits of Lab Automation

Introducing automation addresses several common challenges facing high-throughput genomic labs, such as ensuring consistency and reproducibility. A 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
Learn More About LIMS

Automated Library Preparation Solutions

We partner with leading automation vendors to automate our library prep kits on a range of liquid handlers. These methods eliminate the time and effort required for you to develop your own automation scripts.

Learn More About Library Prep Automation
Reasons for Automating Routine Lab Procedures

New LIMS users highlight how lab automation software helped optimize cumbersome workflows and scale up throughput.

Read Interview

Sequencing Lab Automation

Explore solutions designed to meet the needs of large-scale genomic analysis labs, from production-scale sequencers to multiplexing and more. Hear from scientists who have set up high-capacity sequencing and automated workflows.

Learn More About High-Throughput Sequencing

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 Genotyping
Explore Array Automation Packages
A LIMS Tailored for Genomics Labs

BaseSpace Clarity LIMS is our laboratory information management system. Designed specifically for genomics labs and optimized for NGS, 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, BaseSpace Clarity LIMS is designed with the end user in mind, encouraging wider adoption by lab staff.

View Product

Data 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 with file formats that can be easily shared with collaborators or public databases.

Explore File Formats
Collaborate

Sharing large sets of data can present obstacles involving arcane FTP protocols, hard drive limits, and incompatible device interfaces.

Illumina Connected Analytics and BaseSpace Sequence Hub makes 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.

Sharing Solutions

Apps for genome scale analysis

BaseSpace Sequence Hub Apps simplify genome-scale data for four of the most commonly used biological applications.

Read Data Sheet
BaseSpace Sequencing Hub

The Illumina cloud-based genomics computing environment for NGS data management and analysis. It fosters collaboration and innovation with simplified data sharing.

Learn More
BaseSpace 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.

Learn More

Sample 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) in software that allows you to effectively manage samples and associated data. With this software, your lab can automate workflows and integrate with instruments to improve lab efficiency.

Learn More About LIMS

Simple 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.

For NextSeq Series and MiniSeq Sequencing Systems:

The Prep Tab in BaseSpace Sequence Hub enables simple sample and run management. This software offers an intuitive, graphical environment for one-stop library and run preparation.

For NovaSeq, HiSeq, or MiSeq Sequencing Systems:

The Illumina Experiment Manager software application guides you through the creation of sample sheets before a sequencer run. Built-in validation checks help you minimize sample sheet errors.

Alt Text

Importance of Standards and Quality Control

With rapidly advancing NGS technology, it’s critical to have quality-control checks for the large volumes of data being generated. Illumina provides guidelines for using control DNA standards in sequencing experiments, enabling researchers to maintain confidence in the quality of their data and experiment results.

Learn More

Sequencing File Formats

From FASTQ and BCL file formats to raw sequence file conversion, our tools provide the formats you need for successful secondary or tertiary analysis of NGS data.

Sequencing Experiment Setup

Prep Tab in BaseSpace Sequence Hub, Illumina Experiment Manager, and BaseSpace Clarity LIMS make setting up and running sequencing experiments easier than ever.

Lab Information Management Systems

Undertand what a LIMS is, how it can help genomics labs with sample tracking, workflow automation, and downstream data analysis.