Raising the bar in scalability and accuracy

Watchmaker DNA Library Prep Kits with Fragmentation enable highly sensitive clinical and translational applications to access meaningful insights from a broad range of biological sample types, including ultra-low inputs and FFPE, with an unparalleled combination of accuracy and scalability.

The workflow harnesses the process benefits of enzymatic fragmentation, such as ease of automation, increased scalability, and preservation of low input samples, while mitigating the formation of associated library preparation artifacts, including false chimeric reads and hairpin artifacts, that can convolute variant calling. Further, use of the Equinox polymerase delivers ultra-high-fidelity, low-bias library amplification.

 Key Features and Benefits


  • Somatic mutation calling and other low-frequency variant detection NGS assays, including those utilizing challenging samples such as FFPE
  • Inherited disease sequencing
  • Human whole genome sequencing (WGS), including PCR-free
  • Whole exome sequencing (WES)
  • Single cell analysis
  • Metagenomic analysis
  • Bulk RNA sequencing (using cDNA as input)
  • Viral genome sequencing
  • Microbial WGS


Simplified and easily automated workflow.
Figure 1. Simplified and easily automated workflow. The Watchmaker DNA Library Prep Kit with Fragmentation simplifies library construction by using combined enzymatic steps (FRAG/AT) and a ready-to-use ligation master mix to reduce hands-on time compared to a widely used enzymatic fragmentation kit (Supplier A). The Watchmaker kit was designed with automation in mind with generous overages to ensure sufficient fill volumes for automated library preparation.

Key Performance Data

Reduced sequence artifacts enables high-sensitivity applications

The Watchmaker DNA Library Prep Kit with Fragmentation alleviates many issues associated with sonication, delivering ease of automation and improved scalability, while also mitigating the formation of sequence artifacts, such as false chimeric reads and false SNVs resulting from hairpin artifacts, that are often associated with enzymatic fragmentation. These artifacts convolute the identification of true structural and single nucleotide variants in a sample and especially impact highly sensitive applications, such as low-allele-fraction variant calling1.

1 Thomas Gregory, Apollinaire Ngankeu, Shelley Orwick, Esko A Kautto, Jennifer A Woyach, John C Byrd, James S Blachly, Characterization and mitigation of fragmentation enzyme-induced dual stranded artifacts, NAR Genomics and Bioinformatics, Volume 2, Issue 4, December 2020, lqaa070,

Ultra-high fidelity amplification improves accuracy

The Equinox Library Amplification Master Mix contains a proprietary proofreading polymerase optimized for ultra-high fidelity amplification delivering a 40% reduction in overall polymerase error rate in comparison to a high-fidelity PCR HotStart DNA Polymerase. This enables sensitive variant detection by minimizing overall error rates and reducing false variant calls. The significant reduction in C>T substitutions is particularly important as this mutation is associated with the spontaneous deamination of methylated cytosine to uracil, and is also one of the most common mutation types in cancers.

Robust performance improves utility of clinically relevant sample types

Challenging clinically relevant sample types have historically been difficult to reproducibly process. Vanishingly small input amounts raise the issue of inherent sample loss when using sonication to shear genomic DNA. Formalin-fixed paraffin-embedded (FFPE) samples, while critical to oncology research, are typically highly damaged as a result of the fixation process. The Watchmaker DNA Library Prep Kit with Fragmentation delivers high-quality libraries, exhibiting exceedingly small amounts of adapter-dimer contamination, with ultra-low input amounts and poor sample qualities, improving researchers’ ability to derive meaningful biological interpretations from sequence data.

Tunable fragmentation ensures compatibility with a broad range of applications

The Watchmaker DNA Library Prep Kit with Fragmentation delivers highly tunable DNA fragmentation through modulation of both reaction time and temperature. The wide range of attainable library distributions makes the workflow broadly compatible with a variety of applications and sequencing read lengths.

Uniform sequence coverage improves sequencing economy

Watchmaker DNA Library Prep Kits with Fragmentation delivers even sequence coverage uniformity across complex genomes. This can reduce the amount of overall sequencing – and associated costs – needed to achieve desired coverage depths for all regions of interest.