Watchmaker DNA library preparation
Flexible whole genome library preparation with PCR-free workflows from as little as 100 ng DNA and PCR workflows for lower-input samples.
The Watchmaker DNA Library Preparation Kit is a enzymatic fragmentation-based protocol for preparing high-quality Illumina sequencing libraries from genomic DNA. The protocol is available in both PCR-free and PCR-based workflows, and supports a broad range of input amounts.
The Watchmaker DNA workflow is suitable for applications including WGS, low-pass WGS, and population genomics, particularly for projects with limited DNA amounts.
Sample requirements
- Sample type: Genomic DNA
- Amount: >300ng recommended (see table below)
- Volume: 25–50 µL.
- Sample buffer: Submit samples in EB buffer (Tris-HCl, pH 8.0) or nuclease-free water.
Buffers should be free from EDTA (low concentrations ≤0.1 mM EDTA are acceptable).
! EDTA-based sample buffers may interfere with the enzymatic fragmentation reaction and result in unexpected library insert sizes.
Recommended input
Two library preparation workflows are available depending on the amount of DNA:
| Workflow | Library input | Recommended DNA amount submitted |
| Watchmaker DNA Fragmentation PCR-Free | 100 ng | >300 ng |
| Watchmaker DNA Fragmentation PCR | 10-100 ng* | minimum 50 ng, ideally >300 ng |
*The PCR workflow has been validated with DNA inputs of 10 ng, 50 ng and 100 ng, and has successfully been tested with as little as 1 ng DNA. However, DNA input amounts below 10 ng will impact library performance and data quality.
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.
Concentration
Please use fluorometric measurements (e.g. Qubit, Quant-it), not absorbance measurements (Nanodrop, spectrophotometer).
Checking the quality and purity
The DNA should be of high quality with at least 50% of DNA fragments larger than 1.5 kb, and have an A260/A280 ratio between 1.8 and 2.0.
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 step in which we make sure the sample meets our requirements.
If the samples fail this quality control 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 prep does not work you will have to pay for the library preparation anyway.
If the samples pass quality control, the samples will be queued for library preparation.
Library preparation
The Watchmaker DNA workflow uses enzymatic DNA fragmentation instead of mechanical shearing. DNA fragmentation, end repair and A-tailing are performed in a single combined reaction, simplifying the workflow while allowing fragment size to be tuned by adjusting incubation conditions.
Following fragmentation, Illumina-compatible adapters containing unique dual indexes are ligated before optional PCR amplification. For the PCR-free workflow, the amplification step is omitted.
Library QC and sequencing
We evaluate the concentration of the libraries using qPCR and look at the library fragment size distribution of the library molecules using TapeStation or FragmentAnalyzer. 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.
Expected results
Watchmaker DNA Library Prep is well suited for whole-genome sequencing, including PCR-free WGS. The workflow is designed to minimize sequence bias and artifacts and provides uniform genome-wide coverage even with lower inputs. The reported performance shows improved coverage of challenging GC-rich regions compared with other library preparation workflows.
Price examples
Library preparation cost is ca 1000 SEK per sample. Also see price examples page.
Last Updated: 1st October 2026