NovaSeq 6000 Sequencing System

The NovaSeq 6000 Sequencing System is an integrated ultrahigh throughput system performing onboard cluster generation and sequencing. This system includes installation and training and 12 months warranty (including parts and labor).

NovaSeq 6000 System expands sequencing capabilities by combining throughput, flexibility, and simplicity for virtually any method, genome, and scale.

Tried and true performance

A flexible workflow designed to help you accelerate your research and maximize results

Advanced applications. Impactful discoveries.

Specifications

Output per flow cell for various read lengths

Read length	SP	S1	S2	S4
1 × 35 bp	N/A	N/A	N/A	280–350 Gb
2 × 50 bp	65–80 Gb	134–167 Gb	333–417 Gb	N/A
2 × 100 bp	134–167 Gb	266–333 Gb	667–833 Gb	1600–2000 Gb
2 × 150 bp	200–250 Gb	400–500 Gb	1000–1250 Gb	2400–3000 Gb
2 × 250 bpb	325-400 Gb	N/A	N/A	N/A

Estimated sample throughput for key applications

Application	SP	S1	S2	S4
Human genomes per run	~4	~8	~20	~48
Exomes per run	~40	~80	~200	~500
Transcriptomes per run	~32	~64	~164	~400

Reads passing filter per flow cell

Read type	SP	S1	S2	S4
Single-end reads	650–800M	1.3–1.6B	3.3–4.1B	8–10B
Paired-end reads	1.3–1.6B	2.6–3.2B	6.6–8.2B	16–20B

Quality scores

Read length	SP	S1	S2	S4
1 × 35 bp	N/A	N/A	N/A	≥ 90% of bases higher than Q30
2 × 50 bp	≥ 90% of bases higher than Q30			N/A
2 × 100 bp	≥ 85% of bases higher than Q30
2 × 150 bp	≥ 85% of bases higher than Q30
2 × 250 bp	≥ 75% of bases higher than Q30	N/A	N/A	N/A

Run time

Read length	SP	S1	S2	S4
1 × 35 bp	N/A	N/A	N/A	~14 hr
2 × 50 bp	~13 hr	~13 hr	~16 hr	N/A
2 × 100 bp	~19 hr	~19 hr	~25 hr	~36 hr
2 × 150 bp	~25 hr	~25 hr	~36 hr	~44 hr
2 × 250 bp	~38 hr	N/A	N/A	N/A

Documents

• Human Whole-Genome Sequencing with the NovaSeq 6000 Sequencing System
• NovaSeq 6000 System Quality Scores and RTA3 Software
• The NovaSeq Xp workflow provides flexibility and control without sacrificing data quality or yield
• High-performance whole-genome sequencing with Illumina DNA PCR-Free Prep, Tagmentation
• Illumina Proactive Service connectivity guide - NovaSeq 6000

Support Documentation

• NovaSeq 6000 Sequencing System Guide Documentation
• NovaSeq 6000 Sequencing System Site Prep Guide Documentation
• NovaSeq 6000 Sequencing System Safety and Compliance Guide Documentation
• NovaSeq Series Custom Primers Guide Documentation
• NovaSeq Xp Workflow Checklist Documentation
• All NovaSeq 6000 System Support