NovaSeq

NovaSeq is a high-throughput DNA sequencing platform developed by Illumina, designed to support large-scale genomics projects and to provide scalable throughput that reduces the cost per base. Introduced to address the needs of expansive sequencing studies, it serves as a successor in the Illumina line of SBS-based instruments and is widely used in research and clinical settings.

Technically, NovaSeq relies on sequencing-by-synthesis chemistry with reversible terminators, ExAmp clustering, and patterned flow cells. These features enable a higher density of DNA clusters on the flow cell and improved data quality, along with flexible read lengths and multiplexing through dual indexing. The system integrates sequencing, optics, and software to deliver parallel data generation across multiple samples in a single run.

The platform offers multiple flow cell configurations—S1, S2, and S4—that scale throughput from lower to higher levels. The S4 configuration provides the greatest output, making NovaSeq suitable for very large projects such as whole-genome sequencing, large-scale exome studies, transcriptomics, and metagenomics. Run times and data yield depend on the chosen read length and configuration, with outputs capable of reaching several terabases per run in typical high-throughput setups.

Applications and workflow typically include whole-genome sequencing, exome sequencing, RNA sequencing, targeted panels, and metagenomics. Library preparation and sequencing produce raw data in base calling and FASTQ formats, which are managed by Illumina software such as Local Run Manager or BaseSpace and processed through standard or custom bioinformatics pipelines.

NovaSeq has become a core instrument in many sequencing centers, valued for its speed, scalability, and the ability to handle large sample cohorts in a cost-efficient manner.