The choice of the appropriate sequencing device depends on the targeted data amount. The benefit for you is that we can offer you the right sequencer with the optimal balance of data output, time and costs as several sequencing devices are available at the NGS Core Facility:

NovaSeq 6000

The NovaSeq 6000 is Illumina´s newest sequencing system which is characterized by its flexibility in terms of data output. This sequencer is the ideal sequencing device for high-throughput experiments like whole-genome, exome or whole transcriptome sequencing. By using the latest sequencing by synthesis (SBS) chemistry (v1.5), each flowcell can generate within 2 days up to 3,000 giga bases (Gb) with 2×150 basepairs (bp) read length or up to 10 billion reads per sequencing direction.

NextSeq 550

The NextSeq 550 sequencer offers two flowcells with capacities of 130 and 400 million reads per sequencing direction. With read lengths of 1x75bp to 2x150bp, data sets of 16-120Gb can be generated. This makes the NextSeq 550 the system of choice for small to medium sized sequencing projects. Typical applications are small genome sequencing, targeted gene sequencing and transcriptome sequencing.


The MiSeq sequencer is Illumina´s benchtop solution for small-sized sequencing projects and is the only system which allows a read length of 2x300bp. It is suitable for a broad range of applications like small genome sequencing, targeted gene sequencing (amplicon or gene panel) and metagenomics (16S rRNA). Using the latest version of reagents (v3), up to 15 Gb of output can be generated (with 22-25 million reads per sequencing direction and 2×300 bp read lengths). For smaller projects, a scale-down regarding output and costs is also possible with the previous version of reagents (v2). Therefore, it is possible to adjust the approach according to your needs regarding data output and budget.


Regarding data outcome and costs, the MiniSeq is a good alternative system to the MiSeq. Two flowcell types with specific data capacities of 7 and 22 million reads per sequencing direction makes this sequencer very adjustable for smaller projects like small whole-genome sequencing (microbe or virus), targeted gene sequencing and metagenomics (16S rRNA). Furthermore, the specific rapid flowcell allows fast data generation of 20 million reads with a read length of up to 100bp within less than 5 hours.

iSeq 100

This system is the only sequencer which uses the one-channel sequencing chemistry. The corresponding flowcell generates 4 million single reads with read lengths of up to 2x300bp. The main applications are small whole genome sequencing projects (/microbe, virus) and targeted gene sequencing (amplicon or panel).

Supporting devices

For quality control of samples and preparation of sequencing libraries following devices are used in the NGS Core Facility Bonn:

  • Tapestation 4200 (Agilent Technologies) – DNA/RNA quality control
  • Qubit 4 / Qubit flex (Thermo Fisher Sceintific) – Quantification of DNA/RNA
  • LE-220 plus sonicator (Covaris) – fragmentation of DNA
  • Biomek i7 (Beckman Coulter) – pipetting roboter (exomes, 3´-mRNA, genomes)
  • Chromium Controller (10X Genomics) – diverse single-cell based protocols

All shown pictures of the sequencers are courtesy of Illumina, Inc.