DNA NGS Solutions
Cover your bases at scale
While DNA library preparation has become commonplace in most genomics labs, many challenges related to performance, reliability, and scalability remain — particularly when DNA template is limited or of variable quality. Watchmaker offers streamlined and flexible workflows for both genomic and epigenomic profiling that address all sample types while yielding high conversion rates, reduced bias and artifacts, and reproducible results.
- Watchmaker DNA Library Prep Kits with Fragmentation combine accuracy and scalability for highly sensitive clinical and translational applications, including FFPE analysis
- Watchmaker DNA Library Prep Kits deliver improved coverage and sequencing economy with fragmented DNA, including cfDNA from liquid biopsies
- Watchmaker DNA Library Prep Kits with TAPS+ enable direct 5mC detection for simultaneous genomic and epigenomic profiling with higher CpG coverage and improved alignment
Key Highlights:
- Achieve robust, high-quality performance from FFPE samples, including preserved methylation profiles for accurate downstream analysis
- Maximize sensitivity with cfDNA, enabling reliable detection of low-frequency variants and 5mC methylation from challenging liquid biopsy inputs
- Minimize sequence bias and artifacts for improved accuracy and sensitivity
- Streamlined, automatable workflows generate sequencing-ready libraries from inputs as low as 500 pg
Simple, automatable workflows for all sample types
Figure 1. Simple DNA library prep solutions. Watchmaker’s DNA portfolio offers highly streamlined workflows to address a full range of sample types and applications. Samples requiring fragmentation use a consolidated enzymatic fragmentation and A-tailing (Frag/AT) step, while pre-fragmented inputs (e.g., cfDNA or mechanically sheared DNA) use a combined end-repair and A-tailing (ER/AT) step. For methylation and multimodal analysis, the TAPS+ workflow enables direct detection of 5mC without the harsh chemical treatment of bisulfite-based methods.
Product comparison
| Watchmaker DNA Library Prep Kit with Fragmentation | Watchmaker DNA Library Prep Kit | Watchmaker DNA Library Prep Kit with TAPS+ | |
| Input | dsDNA that requires fragmentation | dsDNA that is already sheared or does not require fragmentation | dsDNA that is already sheared or does not require fragmentation |
|---|---|---|---|
| Input range | < 1 ng to 500 ng | 500 pg – 1 µg | 1 ng to 200 ng |
| Library prep time (excluding PCR) | 1.5 – 2.5 hr (including enzymatic fragmentation) | 2 – 3 hr (from fragmented input) | 6 hr (from fragmented input) |
| Adapter compatibility | Full-length UDI or CDI adapters “Stubby" adapters Adapters with/without UMIs | Full-length UDI or CDI adapters “Stubby" adapters Adapters with/without UMIs | Full-length UDI or CDI adapters “Stubby" adapters Adapters with/without UMIs |
| Supports PCR-free workflows | Yes | Yes | No |
| Single tube library prep | Yes | Yes | No |
| Automation-friendly workflow | Yes | Yes | Yes |
Sample type compatibility
| Watchmaker DNA Library Prep Kit with Fragmentation | Watchmaker DNA Library Prep Kit | Watchmaker DNA Library Prep Kit with TAPS+ | |
| FFPE DNA | X | X | X |
|---|---|---|---|
| Genomic DNA | X | X | X |
| Plasmids and vectors | X | X | X |
| Long amplicons | X | X | |
| cfDNA | X | X | |
| ChIP DNA | X | * | |
| Short PCR products | X |
*Contact support@watchmakergenomics.com.
Application fit
| Watchmaker DNA Library Prep Kit with Fragmentation | Watchmaker DNA Library Prep Kit | Watchmaker DNA Library Prep Kit with TAPS+ | |
|---|---|---|---|
| Whole genome sequencing (human, microbial) | X | X | X |
| Targeted sequencing (hyb. capture) | X | X | X |
| Somatic and germline variant detection | X | X | X |
| Copy number variation (CNV) analysis | X | X | X |
| Detection of translocations and other structural variants | X | X | X |
| cfDNA / ctDNA / liquid biopsy analysis | X | X | |
| Fragmentomics | X | X | |
| Methyl-seq | X* | X | |
| Metagenomic analysis | X | X | X |
| Bulk RNA-seq (from full-length or fragmented cDNA) | X | X | |
| Viral sequencing | X | X | |
| ChIP-seq | X |
*In combination with Equinox Uracil Tolerant Library Amplification Kits.
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