Illumina NovaSeq6000 Sequencing System


The IIHG Genomics Division currently operates the Illumina NovaSeq 6000 sequencing platform. The NovaSeq 6000 is a two flow cell instrument that  is capable of accommodating a variety of run formats which deliver varying sequencing yields, depending on the need of the project (see table below). The ability to run two flow cells concurrently also ensures that priorities for both clinical and research samples are maintained.

As noted in the table below, there are 4 different flow cell options: SP, S1, S2, and S4.  Each flow cell has two lanes, except for the S4 which has four lanes.  Each flow cell type gives a different number of reads per lane and the resulting yield depends on the run format (read length).  Samples are barcoded (indexed) during library preparation to permit the ability to load multiple samples per lane. Please contact the Genomics Division if you have questions about the depth of coverage needed for your project, the most suitable flow cell and run format for your project and how many samples you could combine per lane.  


NovaSeq 6000:  Approximate Yield/Flow Cell Lane

Flow Cell Type (Approximate Reads/Lane)

Run Format


(325-400 M)


(650-800 M)


(1,650-2,000 M)


(2,000-2,500 M)

1 x 100 bp

40 Gb

80 Gb

200 Gb


2 x 50 bp

40 Gb

80 Gb

200 Gb


2 x 100 bp

80 Gb

160 Gb

400 Gb

500 Gb

2 x 150 bp

120 Gb

240 Gb

600 Gb

750 Gb

2 x 250 bp

200 Gb




NA = Not Available



Illumina MiSeq Sequencing System


​The Illumina MiSeq is a “benchtop” sequencer that uses a single lane flow cell capable of yielding one million to 25 million reads per run depending on flow cell type and run format.  The run time ranges from a few hours to three days.  This instrument is recommended for projects that require fast turn-around time but do not require a great number of reads.



MiSeq Reagent Kit v2


MiSeq Reagent Kit v3

Read Length1 x 36 bp2 x 25 bp2x150 bp2 x 250 bp 2 x 75 bp2 x 300 bp
Total Time~4 hrs~5.5 hrs~24 hrs~39 hrs ~21 hrs~56 hrs
Output540-610 Mb750-850 Mb4.5-5.1Gb7.5-8.5 Gb 3.3-3.8 Gb13.2-15 Gb


Contact Information

116 EMRB
Phone: (319) 335-6736

For information about downstream bioinformatics support, contact the IIHG Bioinformatics Division at (319) 335-6717.