Overview

The Illumina NextSeq 500 and NextSeq 550 systems combine the power of high-throughput sequencing with the simplicity of a desktop sequencing instrument.

• High-throughput sequencing—The NextSeq 500 and NextSeq 550 systems enable sequencing of exomes, whole genomes, and transcriptomes and supports TruSeq™, TruSight™, and Nextera™ libraries.
• Flow cell types—Flow cells are available in configurations for high output and mid output. Each flow cell type is kitted with a compatible prefilled reagent cartridge.
• Real-Time Analysis (RTA)—Integrated analysis software performs on-instrument data analysis, which includes image analysis and base calling. The NextSeq uses an implementation of RTA called RTA v2, which includes important architecture and feature differences. For more information, see Real-Time Analysis Overview.
• Cloud-based analysis with BaseSpace Sequence Hub—The sequencing workflow is integrated with BaseSpace Sequencing Hub, the Illumina genomics cloud computing environment for run monitoring, data analysis, storage, and collaboration. As the run progresses, output files are streamed in real-time to BaseSpace Sequencing Hub for analysis.
• On-instrument data analysis— The Local Run Manager software analyzes run data according to the analysis module specified for the run.
• Integrated array scanning in control software—The NextSeq 550 550 allows you to transition between array scanning and high-throughput sequencing on the same instrument and control software.
• Extended imaging capability—The imaging system in the NextSeq 550 550 includes software and stage modifications that enable imaging of a larger surface area to accommodate BeadChip scanning.
• BeadChip types—Compatible BeadChip types include CytoSNP-12, CytoSNP-850K, Karyomap-12, and MethylationEPIC v1.0.
• BeadChip adapter—A reusable BeadChip adapter enables easy loading of a BeadChip onto the instrument.
• Data Analysis—Use the BlueFuse Multi software to analyze array data.

The instructions in this guide are also applicable to the NextSeq 550Dx instrument when in research mode with the latest version of RUO instrument software. For a summary of exceptions and other considerations, see NextSeq 550Dx Research Mode Considerations.