upSPLAT: Upscale SPLAT for Cost-effective Large-scale Sequencing
Cost-efficient, high-throughput library preparation for whole-genome sequencing of large sample collections. Only for sample batches of 96.
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
- Only available in batches of 96 samples
- Amount: >300ng recommended
- Concentration: ≥10 ng/µL.
- Samples with concentrations <10 ng/µL can be difficult to normalize accurately, which may lead to greater variation in sample representation within the pool.
- Volume: 25-50 µl (water or EB buffer)
- DNA should preferably be of high quality.
- Input amount for preparing one library: 50 ng DNA per sample
Please contact our Project Coordinators if the sample requirements cannot be fulfilled.
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.
We recommend submitting DNA samples at concentrations ≥10 ng/µL to ensure reliable quantification and normalization before library preparation.
Samples with concentrations below 10 ng/µL can still be processed; however, accurate quantification and normalization become more challenging at lower concentrations, which may result in greater variation in sample representation within a pool. Please contact our Project Coordinators if the sample requirements cannot be fulfilled.
Degraded DNA
Degraded DNA can be suitable for upSPLAT and may not require initial Covaris fragmentation.
Therefore, assessing DNA integrity, for example by agarose gel, is recommended. However, DNA concentration should preferably still be ≥10 ng/µL. Samples within the same pool (16 samples) should have similar levels of degradation.
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 input 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.
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.
Price examples
The cost for library prep 1 plate (total 96 samples) is around 19 700 SEK.
Last Updated: 2nd October 2026