NextSeq

NextSeq is a line of benchtop DNA sequencing instruments from Illumina, designed for mid- to high-throughput sequencing in research and clinical laboratories. The platforms are intended to fill the gap between lower-throughput systems like MiSeq and high-throughput platforms like HiSeq and NovaSeq, offering variable throughput and read configurations for diverse applications such as whole-genome sequencing of small genomes, exome and targeted sequencing, RNA-Seq, and amplicon sequencing.

Technology and workflow: NextSeq uses Illumina's sequencing-by-synthesis chemistry with fluorescently labeled nucleotides and optics to read cycles of base incorporation. DNA libraries are attached to a flow cell to form clusters, enabling base calling, and data are delivered as FASTQ files with quality scores. The platform supports paired-end sequencing and configurable read lengths depending on kit and model.

Models and throughput: The NextSeq family includes NextSeq 500/550 and higher-throughput NextSeq 1000/2000 variants. Configurations balance run time, read length, and data output; typical read lengths reach up to 2x150 bp, with shorter reads common for targeted panels or expression profiling. Runs can be short to moderate in duration.

Software and outputs: Onboard analysis software and integration with Illumina's DRAGEN pipelines or BaseSpace allow base calling, alignment, and variant calling, with results exported in standard formats such as FASTQ, BAM, and VCF. Data can be analyzed locally or in cloud-based workflows.

Impact and limitations: NextSeq devices are widely used for targeted sequencing, exome sequencing, and transcriptomics due to their balance of throughput and cost. Compared with larger platforms, they offer lower maximum capacity and higher per-base cost for very large projects. See also HiSeq, NovaSeq, and MiSeq.