Data production can reach up to 20,000 million (M) paired-end reads per sequencing run; the NovaSeq 6000 has the capacity to sequence 2 flowcells at the same time. Read lengths can vary between 50 and 250 base pairs. There are 4 types of flowcells (SP, S1, S2, and S4) with data production rates per sequencing lane ranging from 400 to 2,500 million paired-end reads.
| SP | S1 | S2 | S4 | |
| Per Lane | ||||
| Clusters*/lane – MIN | 325 M | 650 M | 1650 M | 2,000 M |
| Clusters/lane – MAX** | 400 M | 800 M | 2,000 M | 2,500 M |
| 1X 35 bp | na | na | na | 350 Gb |
| 2X 50 bp | 40 Gb | 80 Gb | 200 Gb | na |
| 2X 100 bp | 80 Gb | 160 Gb | 400 Gb | 500 Gb |
| 2X 150 bp | 120 Gb | 240 Gb | 600 Gb | 750 Gb |
| 2X 250 bp | 200 Gb | na | na | na |
| Per Flowcell | ||||
| Number of Lanes | 2 | 2 | 2 | 4 |
| Total MAX Clusters | 800 M | 1,600 M | 4,000 M | 10,000 M |
*Clusters: Number of sequenced fragments. Yield may vary.
** May vary depending on multiplexing and library type
| SP | S1 | S2 | S4 | |
| Example of Number of Samples per Lane* | ||||
| mRNA (20M 100bp PE-reads) | 18 | 38 | 90 | 112 |
| Total RNA (30M 100bp PE-reads) | 12 | 25 | 60 | 75 |
| microRNA (10M 100bp PE-reads) | 36 | 75 | 185 | 225 |
| Metagenomes (7 Gb) | 16 | 32 | 78 | 96 |
| Human Genomes | 2 | 5 | 12 | |
| Run Time | 19-25 hours | 19-25 hours | 25-36 hours | 36-44 hours |
*Standard coverage