Informatics

Sequencing data analysis

Find intuitive NGS data analysis solutions that allow you to spend more time doing research and less time setting up workflows

Male scientist analyzing a monitor on a laptop, not visible, in a lab setting.

User-friendly NGS data analysis tools

Sequencing generates large volumes of data, and the analysis required can be intimidating. Fortunately, the analytical tools available today take most of the manual work out of the next-generation sequencing (NGS) data analysis process, making it easier for you to glean meaningful insights quickly.

User-friendly Illumina informatics tools smooth the process of analyzing sequencing data, so you can spend more time doing research and less time configuring workflows. Our NGS software packages perform analysis after the on-instrument data processing is complete for optimized turnaround times.

Sequencing data analysis process

The NGS data analysis process includes three main steps: primary, secondary, and tertiary data analysis. Some steps are performed automatically on the sequencing instrument, while other steps occur after sequencing is completed.

Primary data analysis

Real-Time Analysis (RTA) software operates during cycles of sequencing chemistry and imaging, providing base calls and associated quality scores representing the primary structure of DNA or RNA strands. This built-in software performs primary data analysis on Illumina sequencing systems automatically.

Secondary data analysis

Secondary analysis tools align and assemble DNA and RNA fragments, providing the full sequence for a sample, from which genetic variants can be determined.

DNA sequencing data analysis

We offer intuitive bioinformatics tools for ultrarapid secondary analysis, simplifying variant calling and data visualization.

RNA sequencing data analysis

Our user-friendly software tools simplify NGS data analysis for a broad range of RNA sequencing experiments, from gene fusion detection to total RNA expression profiling.

Tertiary data analysis

From sequence data, you can use biological data mining and interpretation tools to convert data into knowledge.

Biological data interpretation

Interpreting genetic variation provides research insights into basic biological processes, novel genetic biomarkers, and the causes of diseases.

Get started with NGS data analysis

Explore our introduction to sequencing data analysis for new users eBook and learn how to leverage NGS data to unlock biological insights. This eBook covers how to get started with bioinformatics, steps in a typical NGS workflow, available applications, and analysis.

Featured sequencing data analysis solutions

DRAGEN secondary analysis

Perform fast, robust secondary analysis of NGS data. Analyze sequencing data from whole genomes, whole exomes, germline, and somatic data sets, RNA sequencing experiments, and more.

Illumina Connected Multiomics

Leverage cloud-based multiomic analysis and interpretation software to enable sample-to-insight workflows with interactive visualizations, infrastructure scalability, and secure data management.

Illumina Connected Analytics

Operationalize bioinformatics workflows with sequencer integration, automatic analysis of customizable workflows, or out-of-the-box DRAGEN pipelines.

Advancing genomic research with AI

Learn how artificial intelligence (AI) is transforming genomics by offering advanced tools to analyze and interpret complex genetic and multiomic data.

Genomic data storage and security

Store, process, and share large quantities of NGS and other genomic data securely in the cloud with built-in speed and scalability.

NGS data analysis articles

Streamlining NGS data analysis and storage

An Oxford scientist discusses her decision to move NGS data analysis to the cloud and the benefits it has given her lab, including increased productivity and cost-effectiveness.

NGS Workflow Finder

Take the guesswork out of your next workflow. The NGS Workflow Finder provides personalized solution recommendations and resources so you can sequence with confidence.

Find your NGS workflow today

NGS data analysis tips for new users

Sequencing data examples

Explore sample data generated on Illumina sequencing systems. These examples help you understand sequencing data and analysis reports.

DNA sequencing data examples
RNA sequencing data examples

File formats for NGS data

Sequencing data can be represented with a variety of file formats, many of which are interchangeable, and your informatics system needs to be able to handle the formats you’ll use.

Learn more about sequence file formats
Thumbnail

Sequencing data analysis: Introduction to key concepts

Join our technical experts as they provide experimental design, key bioinformatics concepts, and Illumina software tools to improve your data analysis experience.

Additional resources

Software support

Access resources and support for Illumina software, including sequencing data analysis and other software tools.

Online training courses

View free online technical training courses that cover common topics in library prep, sequencing, and data analysis.

NGS data analysis FAQ

To make sense of the massive amount of data produced by a sequencer, the sequencing data analysis workflow progresses from raw signals to biological meaning. NGS data analysis includes three main steps: primary, secondary, and tertiary data analysis. Primary analysis converts raw signals into base calls, quality scores, and sequence reads. Secondary analysis processes these reads through demultiplexing, alignment, and variant calling to generate genomic data. Tertiary analysis interprets the resulting variants to deliver biological insights.

Explore our related resource pages to learn more about DNA sequencing data analysis and RNA sequencing data analysis solutions.

The main steps in an NGS data analysis workflow typically include the conversion of raw instrument output into FASTQ files. Subsequent data preprocessing with quality control and trimming is used to clean reads and align the sequences to a reference genome with variant calling for DNA‑Seq data analysis or quantification for RNA‑Seq data analysis. The processed data is then interpreted to infer biological insights.

Learn more about NGS workflow steps.

Yes, Illumina offers multiple NGS data analysis tutorials and on-demand webinars to help you get started.

View our NGS tutorials to learn about sequencing workflows, sample prep, data analysis, and more.

Yes, Illumina provides reference genome data for DRAGEN secondary analysis. Customers can download the reference genomes from the support page.

/ Results

Speak to a specialist

Talk to an expert to learn more about sequencing data analysis solutions.