SPlinted Ligation Adapter Tagging (BSK-SPLAT) for Whole Genome Bisulphite Sequencing (WGBS)

SPLAT is an in-house developed WGBS library preparation method. This approach enables quick and efficient preparation of WGBS libraries from low-input DNA

Our R&D unit at NGI has developed an efficient and cost-effective approach for Whole-Genome Bisulfite Sequencing (WGBS) library preparation. This method, called SPLinted Adaptor Tagging (BSK-SPLAT), has the major advantage of uniform coverage of the genome. The method is based on bisulfite treatment of DNA followed by adapter tagging of single-stranded DNA fragments, enabling high-quality WGBS from low DNA input amounts.

The article presenting this method, including a detailed laboratory protocol, was published online in Nucleic Acids Research on November 28, 2016. The article presents validation of BSK-SPLAT against three commonly used WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adapter tagging and one is a conventional WGBS method. Read the article to learn more.

For more information regarding this technique, please contact our project coordinators.

How to evaluate the sample quality

We check samples upon arrival; however, we strongly recommend that users perform their own quality control prior to shipment.

Checking the concentration
Please use fluorometric measurements (e.g. Qubit, Quant-it), not absorbance measurements (Nanodrop, spectrophotometer).

Checking the quality and purity
The DNA should be in water or EB buffer, of high quality, and ideally have an OD260/280 of 1.8-2. Samples must be RNA-free. Contaminating RNA may affect the efficiency of the library preparation.

If you are not able to carry out these steps, or your samples are below the required thresholds, please get in touch.

What we do with your samples

Once your samples arrive at NGI, we start by performing a quality control (QC) step in which we make sure the samples meet our requirements.

If the samples fail this QC step, we will contact you to discuss possible options. Should you choose to proceed with samples not fulfilling the criteria it will be at your own risk, NGI will only make one attempt at library preparation and if the library preparation does not work you will be charged for the library preparation regardless.

If the samples pass QC, the samples will be queued for library preparation.

Library Preparation

DNA is spiked with unmethylated lambda DNA, fragmented by Covaris, bisulfite converted, denatured, and ligated to adapters using a single-stranded DNA ligation strategy, followed by bead-based cleanup steps. Libraries are PCR amplified with unique dual indexes and purified to generate sequencing-ready libraries.

Unmethylated lambda DNA is added as an internal control to assess bisulfite conversion efficiency and enable quality control of methylation calls.

Library QC and Sequencing

We evaluate the concentration of the libraries using qPCR and look at the fragment size distribution of the library molecules. Once the libraries have passed this QC step, they are normalised, pooled, and queued for sequencing.

The sequencing will be carried out following the setup stated in the agreement.

Last Updated: 28th January 2026