Illumina NextSeq 2000 Sequencing

Four types of flow cell options, the P1, P2, P3, and P4, are available with a range of outputs to accommodate a wide variety of NGS projects. The P4 is a high-output flow cell that generates up to 1.8 billion reads per run. At 100 million reads per run, the P1 flow cell is an attractive option for viral and pathogen sequencing, “smaller” batch RNA-Seq, targeted panels, and more.

The primary advantages of the NextSeq 2000 are the sequencing speed and multiple run configurations that enable a range of sequencing outputs.

Five run configurations are available: the 100-cycle kit, the 200-cycle kit, the 300-cycle kit, the 600-cycle kit, and the 50-cycle kit, which is available in the P4 only. The added 50-cycle kit targets infectious disease, small RNA, and spatial transcriptomics applications. 

In addition, users have the benefit of not needing to wait to fill a large, multi-lane flow cell (NovaSeq) before data can be generated. Whether it is the P1, P2, P3, or the P4 flow cell, researchers purchase the full NextSeq flow cell (no lane splitting) and sequencing will begin once libraries are complete and the instrument is available. 

Due to the 2-channel chemistry, the NextSeq does not tolerate low diversity libraries as well as the MiSeq 4-channel platform, and in order to generate high-quality data, a higher spike-in concentration of a diverse control library is required. Thus, amplicon libraries with low sequence diversity should be designed with phasing bases to frameshift low-diversity regions.

In addition, output capacity for custom libraries, including amplicon libraries and low-diversity applications, may generate up to 25% less data in an effort to improve data quality.