upSPLAT: Upscale SPLAT for Cost-effective Large-scale Sequencing
Cost-efficient, high-throughput library preparation for whole-genome sequencing of large sample collections.
upSPLAT (Upscale SPLinted Ligation Adapter Tagging) is an in-house developed library preparation method designed for highly cost-effective sequencing of large sample collections. By introducing sample-specific barcodes early in the workflow, samples can be pooled prior to library completion, significantly reducing both reagent consumption and hands-on time while maintaining quality sequencing results. The method is particularly well suited for projects involving many samples and small to medium-sized genomes. For more information read our preprint.
Key Features
- Cost-efficient library preparation through early sample pooling
- Standard 16-plex library preparation workflow
- Compatible with a broad range of DNA sample types
- Suitable for whole genome sequencing, low-pass sequencing, metagenomics and other large-scale sequencing applications
Sample requirements
- Sample type: gDNA
- Recommended volume: 25-50 µL
- DNA should preferably be of high quality and dissolved in water or EB buffer
- Preferred concentration: ≥10 ng/µL
- Preferred input amount: 50 ng DNA per sample
- Alternative input: 25 ng DNA per sample for smaller genomes or limited material. Please contact our Project Coordinators to discuss your specific requirements
How to evaluate the sample quality
We strongly recommend measuring DNA concentration using fluorometric methods (e.g. Qubit or Quant-iT) rather than absorbance-based methods. Degraded DNA can be suitable for upSPLAT, but samples within the same pool (16 samples) should have similar levels of degradation. Therefore, assessing DNA integrity, for example by agarose gel, is recommended.
What we do with your samples
After sample arrival, we perform quality control to verify DNA concentration. If samples do not meet the recommended requirements, we will contact you to discuss possible alternatives. Samples that proceed despite not fulfilling the recommended criteria may produce uneven pooling and sequencing coverage. TapeStation/Fragment Analyzer assessment of DNA integrity is not included but can be added upon request at an additional cost.
Library preparation
Our standard workflow uses 50 ng DNA per sample. DNA is normalized prior to Covaris fragmentation, which may be omitted for degraded DNA. After this the DNA is transferred directly into the upSPLAT library preparation workflow, where each sample receives a unique inline barcode. Following barcoding, samples are pooled and the remaining library preparation steps are performed on the pooled material.
For samples with very limited DNA amounts (25-50 ng total), fragmented DNA can be concentrated prior to library preparation using a SpeedVac. While feasible, this approach might result in increased variation in sample representation within the pool.
Samples below 10 ng/µL
Samples with concentrations below 10 ng/µL can still be processed, but users should be aware that:
- Accurate normalization becomes difficult
- Pool representation may become uneven
- Some samples may receive substantially lower sequencing coverage than expected
Library QC and sequencing
Completed libraries are quantified using qPCR and evaluated prior to sequencing. Libraries that pass quality control are normalized, pooled where appropriate, and sequenced according to the agreed sequencing setup.
Expected results
Sequencing data will be delivered as demultiplexed fastq files per sample.
Price examples
The cost for library prep 1 plate (total 96 samples) is around 19 700 SEK.
Last Updated: 24th September 2026