We are excited to announce the incorporation of Illumina’s NovaSeq 6000 into the Advanced Genomics Core’s stable of sequencing instruments. As a testament to the cutting-edge nature of U-M research, ours is one of the first academic core facilities to house this exciting and powerful technology. A wide variety of libraries – including whole genome, whole exome, mRNA, ribo-depleted RNA, ATAC, WGBS and more – are now routinely sequenced on the NovaSeq. We have also transitioned our 10X Chromium Single Cell workflow to NovaSeq.

We are revising our procedures to ensure that you maximally benefit from the efficiency, data quality, and cost savings of the NovaSeq. Beginning Monday, April 1, 2019, you will encounter a new sample submission process. You will select the number of cycles and total reads you require for your submission (no more lanes!). Libraries prepped in the core will use unique dual indices to help prevent index collisions and hopping and to help you to share flow cells. We strongly encourage users making their own libraries to also incorporate a dual indexing strategy. When protocols are not amenable to dual indices, please reach out to discuss best practices.

As always, we are happy to help you plan your experiments to make best use of the enhanced capabilities of the NovaSeq – we think you’re going to like it. Please contact seqcore-help@umich.edu with any questions. Also, please check out our NGS FAQs.

Thank you for choosing the U-M Advanced Genomics Core for your genomics needs.

Olivia Koues, Managing Director
Tom Wilson, Faculty Director
U-M Advanced Genomics Core


The NovaSeq 6000 combines 2 color SBS chemistry with the nanowell patterned flow cell. There are four flow cells options, SP, S1, S2, and the S4. There are two different ways to load the Flow cell, individual lane loading (XP) so as to run various experiments on the same flow cell or whole flow cell loading for one experiment across all lanes for greater coverage. We have compiled Illumina specifications for the NovaSeq in the tables below. To see a list of common and compatible sequencing methods for the NovaSeq 6000 visit Illumina’s website or reach out to the DNA Sequencing core for help with your project.

Flow cell Type Paired-End Reads Read length Output Quality Scores Run Time
SP 800 million
100 cycles 65-80 GB ≥85% ~13 hr
300 cycles 200-250 Gb ≥75% ~25 hr
500 cycles 325-400 Gb ≥75% ~38 hr
S1 1.8 billion
100 cycles 134-167 Gb ≥85% ~13 hr
200 cycles 266-333 Gb ≥80% ~19hr
300 cycles 400-500 Gb ≥75% ~25hr
S2 3.6 billion 100 cycles 333-417 Gb ≥85% ~16hr
200 cycles 667-833 Gb ≥80% ~25hr
300 cycles 1000-1250 Gb ≥75% ~36hr
S4 10 billion 200 cycles 1600-2000Gb ≥80% ~36hr
300 cycles 2400-3000 Gb ≥75% ~45hr

For More Information

You can read more about the NovaSeq 6000 specs at the Illumina web site.

Updated 3/19/19 – OKoues