Next Generation Sequencing
NGS platforms and additional services
USEQ 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:
- 1x NextSeq500
- 2x NextSeq2000
- 1x iSeq100
- 2x NovaSeq 6000 (external)
- Nanopore MinIon
- Nanopore GridIon X5
- Nanopore ProMethion
- 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
Pricing
| Service | Price per | Price (excl VAT) |
|---|---|---|
| Nanopore Flongle | Run | € 420 |
| Nanopore MinIon | Run | € 966 |
| Nanopore PromethIon | Run | € 2.009 |
| iSeq 100 (4 M clusers; all configs) | Run | € 1.154 |
| NextSeq500 2 x 75 bp mid output (120 M clusters) | Run | € 1.696 |
| NextSeq500 2 x 150 bp mid output (120 M clusters) | Run | € 2.312 |
| NextSeq500 1 x 75 bp high output (400 M clusters) | Run | € 2.068 |
| NextSeq500 2 x 75 bp high output (400 M clusters) | Run | € 3.342 |
| NextSeq500 2 x 150 bp high output (400 M clusters) | Run | € 4.948 |
| NextSeq2000 2 x 50 bp (P1 -100 M clusters) | Run | € 1.440 |
| NextSeq2000 2 x 150 bp (P1 -100 M clusters) | Run | € 1.717 |
| NextSeq2000 2 x 300 bp (P1 -100 M clusters) | Run | € 2.290 |
| NextSeq2000 2 x 50 bp (P2 -400 M clusters) | Run | € 1.888 |
| NextSeq2000 2 x 100 bp (P2 -400 M clusters) | Run | € 2.954 |
| NextSeq2000 2 x 150 bp (P2 -400 M clusters) | Run | € 3.697 |
| NextSeq2000 2 x 300 bp (P2 -400 M clusters) | Run | € 4.030 |
| NextSeq2000 1 x 50 bp (P3-1000M clusters) | Run | € 2.596 |
| NextSeq2000 2 x 50 bp (P3-1000M clusters) | Run | € 3.450 |
| NextSeq2000 2 x 100 bp (P3-1000M clusters) | Run | € 4.516 |
| NextSeq2000 2 x 150 bp (P3-1000M clusters) | Run | € 5.797 |
| NovaSeq SP 2 x 50 (750M clusters) | Run | € 3.209 |
| NovaSeq SP 2 x 100 (750M clusters) | Run | € 3.854 |
| NovaSeq SP 2 x 150 (750M clusters) | Run | € 4.102 |
| NovaSeq SP 2 x 250 (750M clusters) | Run | € 5.292 |
| NovaSeq S1 2 x 50 (1500M clusters) | Run | € 4.945 |
| NovaSeq S1 2 x 100 (1500M clusters) | Run | € 5.937 |
| NovaSeq S1 2 x 150 (1500M clusters) | Run | € 6.335 |
| NovaSeq S2 2 x 50 (3500M clusters) | Run | € 8.319 |
| NovaSeq S2 2 x 100 (3500M clusters) | Run | € 10.056 |
| NovaSeq S2 2 x 150 (3500M clusters) | Run | € 10.651 |
| NovaSeq S4 1 x 35 (9000M clusters) | Run | € 11.544 |
| NovaSeq S4 2 x 100 (9000M clusters) | Run | € 13.581 |
| NovaSeq S4 2 x 150 (9000M clusters) | Run | € 15.002 |
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.
| Configuration | Run type | Raw reads / pairs (million) |
|---|---|---|
| Mid Output | 2 x 75 bp | 120 |
| Mid Output | 2 x 150 bp | 120 |
| High Output | 1 x 75 bp | 350 |
| High Output | 2 x 75 bp | 350 |
| High Output | 2 x 150 bp | 350 |
Illumina NovaSeq X
Applications: large scale genome, exome, transcriptome sequencing.
| Configuration | Run type | Raw reads / pairs (billion) |
|---|---|---|
| 10B | 2 x 50 bp | 10 |
| 10B | 2 x 100 bp | 10 |
| 10B | 2 x 150 bp | 10 |
ILlumina novaseq 6000
Applications: large scale genome, exome, transcriptome sequencing.
| Configuration | Run type | Raw reads / pairs (million) |
|---|---|---|
| SP | 2 x 50 bp | 750 |
| SP | 2 x 150 bp | 750 |
| SP | 2 x 250 bp | 750 |
| S1 | 2 x 50 bp | 1.500 |
| S1 | 2 x 100 bp | 1.500 |
| S1 | 2 x 150 bp | 1.500 |
| S2 | 2 x 50 bp | 3.500 |
| S2 | 2 x 100 bp | 3.500 |
| S2 | 2 x 150 bp | 3.500 |
| S4 | 2 x 100 bp | 9.000 |
| S4 | 2 x 150 bp | 9.000 |
ILlumina iSeq 100
Applications: small scale amplicon sequencing,Novaseq pooling and rebalancing.
| Configuration | Run type | Raw reads / pairs (million) |
|---|---|---|
| standard | 1 x 36 bp | 4 |
| standard | 1 x 50 bp | 4 |
| standard | 1 x 75 bp | 4 |
| standard | 2 x 75 bp | 4 |
| standard | 2 x 150 bp | 4 |
Illumina NextSeq2000
Applications: genome, exome, transcriptome sequencing.
| Configuration | Run type | Raw reads / pairs (million) |
|---|---|---|
| P1 | 2 x 50 bp | 100 |
| P1 | 2 x 150 | 100 |
| P1 | 2 x 300 | 100 |
| P2 | 2 x 50 bp | 400 |
| P2 | 2 x 100 bp | 400 |
| P2 | 2 x 150 bp | 400 |
| P2 | 2 x 300 bp | 400 |
| P3 | 1 x 50 bp | 1000 |
| P3 | 2 x 50 bp | 1000 |
| P3 | 2 x 100 bp | 1000 |
| P3 | 2 x 150 bp | 1000 |
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 useq@umcutrecht.nl.