Next Generation Sequencing

NGS platforms and additional services

next generation sequencingUSEQ operates a broad range of sequencing platforms, each with unique characteristics. Technical and cost characteristics determine the best fit for your experiment. Service fees include costs for chemicals, operator time, quality control, maintenance, lab information management system (LIMS) and troubleshooting.

Platform & Configurations

Currently, we operate the following Illumina platforms and configurations:

  • NextSeq500 (3 machines)
  • MiSeq (1 machine)
  • MiniSeq (1 machine)

For larger projects, we have access to:

  • NovaSeq 6000 (2 machines)
  • Nanopore MinIon (6 machines)
  • Nanopore GridIon X5 (1 machine)
  • Nanopore PromethIon (1 machines)

On this page you can find an overview per platform of the most widely used run modi, configurations and expected output*. Other run modi and custom recipes are possible as well, upon consultation with USEQ.

* Please note that high quality of sequence libraries is crucial in order to obtain maximum output. For samples submitted as ready to sequence libraries, USEQ cannot take any responsibility for data quality and quantity.

Sample Requirements & Turn around times

For ready-to-sequence samples: please deliver your (pooled) samples in an 1,5 ml tube with a concentration of 4 nM and a minimal volume of 40 ul.

For DNA / RNA library preparation: please refer to the library preparations page.

Turnaround times depend on the specific service; details are described in our FAQ


ServicePrice perPrice (excl VAT)
Nanopore FlongleRun € 223
Nanopore MinIonRun € 843
Nanopore PromethIonRun € 2.343
iSeq 100 (all configs)Run € 893
MiSeq 2 x 150 bp V2 nano kitRun € 750
MiSeq 2 x 150 bp V2 micro kitRun € 878
MiSeq 1 x 50 bp V2 kitRun€ 1.207
MiSeq 2 x 150 bp V2 kitRun€ 1.408
MiSeq 2 x 250 bp V2 kitRun€ 1.519
MiSeq 2 x 300 bp V3 kitRun€ 1.832
MiSeq 2 x 75 bp V3 kitRun€ 1.285
NextSeq500 2 x 75 bp mid outputRun€ 1.437
NextSeq500 2 x 150 bp mid outputRun€ 2.012
NextSeq500 1 x 75 bp high outputRun€ 1.786
NextSeq500 2 x 75 bp high outputRun€ 2.970
NextSeq500 2 x 150 bp high outputRun€ 4.460
NextSeq2000 2 x 50 bp (P2)Run€ 1.629
NextSeq2000 2 x 100 bp (P2)Run€ 2.627
NextSeq2000 2 x 150 bp (P2)Run€ 3.661
NovaSeq SP 2 x 50Run€ 2.770
NovaSeq SP 2 x 100Run
NovaSeq SP 2 x 150Run€ 4.048
NovaSeq SP 2 x 250Run€ 5.365
NovaSeq S1 2 x 50Run€ 4.247
NovaSeq S1 2 x 100Run€ 5.365
NovaSeq S1 2 x 150Run€ 6.244
NovaSeq S2 2 x 50Run€ 8.560
NovaSeq S2 2 x 100Run€ 11.355
NovaSeq S2 2 x 150Run€ 13.152
NovaSeq S4 2 x 100Run€ 26.511
NovaSeq S4 2 x 150Run€ 30.411

Service fees include costs for chemicals, operator time and troubleshooting.

Sample Submission

We provide an online samplesubmission system that is connected to our laboratory management system. PI-groups have an account ID, and all users belonging to this account will have their own user ID for the system. PI's can connect multiple project codes to their account so that billing requires the least administration. Users can submit the sample information online as well and when this is completed, physically hand in the samples in the USEQ freezer at the stratenum. For more details, and the submission procedure, go to the sample submission page

NGS platforms and additional services

Illumina NextSeq500

Applications: genome, exome, transcriptome sequencing.

ConfigurationRun type Raw reads / pairs (million)
Mid Output2 x 75 bp120
Mid Output2 x 150 bp120
High Output1 x 75 bp350
High Output2 x 75 bp350
High Output2 x 150 bp350

Illumina MiSeq

Applications: targeted amplicon and small genome sequencing with longer reads.

ConfigurationRun type Raw reads / pairs (million)
Reagent kit V2 (nano)2 x 150 bp1
Reagent kit V2 (micro)2 x 150 bp4
Reagent kit V21 x 50 bp12
Reagent kit V22 x 150 bp12
Reagent kit V21 x 250 bp12
Reagent kit V32 x 75 bp20
Reagent kit V32 x 300 bp20

ILlumina novaseq 6000

Applications: large scale genome, exome, transcriptome sequencing.

ConfigurationRun type Raw reads / pairs (million)
SP2 x 50 bp750
SP2 x 150 bp750
SP2 x 250 bp750
S12 x 50 bp1.500
S12 x 100 bp1.500
S12 x 150 bp1.500
S22 x 50 bp3.500
S22 x 100 bp3.500
S22 x 150 bp3.500
S42 x 100 bp9.000
S42 x 150 bp9.000

ILlumina iSeq 100

Applications: small scale amplicon sequencing,Novaseq pooling and rebalancing.

ConfigurationRun type Raw reads / pairs (million)
standard1 x 36 bp4
standard1 x 50 bp4
standard1 x 75 bp4
standard2 x 75 bp4
standard2 x 150 bp4

Illumina NextSeq2000

Applications: genome, exome, transcriptome sequencing.

ConfigurationRun type Raw reads / pairs (million)
P22 x 50 bp400
P22 x 100 bp400
P22 x 150 bp400
P3 (Q4 2020)2 x 50 bp1000
P3 (Q4 2020)2 x 100 bp1000
P3 (Q4 2020)2 x 150 bp1000

Oxford Nanopore Sequencing

The third generation sequencing is developing fast. Besides the imaging based real time single molecule sequencing, nanopore sequencing is the new promising technology. We are currently exploring and offering nanopore sequencing using the MinION platform from Oxford Nanopore Technologies in collaboration with the group of Jeroen de Ridder at the UMCU.

Because Nanopore technology is developing fast, please contact us for the latest specifications, performance, and expectations.

Whole Genome Sequencing

We provide access to Human Whole Genome Sequencing (WGS) or other large scale sequencing experiments on the Novaseq 6000 platform.

For further information, please contact us.

Consultancy Service

For expert advice on your NGS-based research and the possibilities USEQ offers to get the most out of your samples: request a meeting at our consulting hour, each Friday at 1:30pm. Experimental design, technology, platform and library preparation choice, standard bioinformatics analysis, results and follow-up experiments are discussed. The facility manager ensures to bring the right experts from any of the participating organisations to the table.

You can request a meeting at


Nanopore sequencing now available; please contact us for the options!
Due to corona preventive measures we could experience some delays. We will try to minimize it. Apologies for this.
Due to corona preventive measures, sample dropoff access is limited to UMCU staff only. If you are from other institutes, please contact useq and make an appointent so we can personally accept your samples.
NEW: we will add nanostring nCounter to USEQ services in the next few weeks!
PRICE UPDATE: from april 21st we have new prices! Generally 6% lower than 2019.