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 two streamlined and flexible workflows 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
Key Highlights:
- Reduce sequence bias and artifacts to improve accuracy and sensitivity
- Improve coverage of low-frequency variants in cfDNA from liquid biopsies
- Rapidly prepare libraries in under 2 hours with as little as 500 pg
- Robust and consistent enzymatic fragmentation simplifies library prep from FFPE and low-inputs
Simple, automatable workflows for all sample types
Figure 1. Simple DNA library prep solutions. Watchmaker’s DNA portfolio offers highly streamlined workflows to address all DNA sample types. Samples requiring fragmentation use a consolidated enzymatic fragmentation and A-tailing step (Frag/AT), while pre-fragmented samples (e.g., cfDNA or mechanically sheared DNA) use a combined end-repair and A-tailing step (ER/AT). Amplifiable libraries may be prepared in approximately 1.25 to under 2 hours, respectively. For applications requiring PCR, Equinox polymerase provides excellent fidelity and yields while only adding about 1 hour to the overall workflow.
Product comparison
| Watchmaker DNA Library Prep Kit with Fragmentation | Watchmaker DNA Library Prep Kit | |
| Input | dsDNA that requires fragmentation | dsDNA that is already sheared or does not require fragmentation |
|---|---|---|
| Input range | < 1 ng to 500 ng | 500 pg – 1 µg |
| Library prep time (excluding PCR) | 90 – 140 min (including enzymatic fragmentation) | 115 – 170 min (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 |
| Supports PCR-free workflows | Yes | Yes |
| Single tube library prep | Yes | Yes |
| Tunable size selection | Optional | Optional |
| Automation-friendly workflow | Yes | Yes |
Sample type compatibility
| Watchmaker DNA Library Prep Kit with Fragmentation | Watchmaker DNA Library Prep Kit | |
| FFPE DNA | X | X |
|---|---|---|
| Genomic DNA | X | X |
| Plasmids and vectors | X | X |
| Long amplicons | X | X |
| cfDNA | X | |
| ChIP DNA | X | |
| Bisulfite-converted DNA* | X | |
| Short PCR products | X |
*In combination with Equinox Uracil Tolerant Library Amplification Kits.
Application fit
| Watchmaker DNA Library Prep Kit with Fragmentation | Watchmaker DNA Library Prep Kit | |
|---|---|---|
| Whole genome sequencing (human, microbial) | X | X |
| Targeted sequencing (hyb. capture) | X | X |
| Somatic and germline variant detection | X | X |
| Copy number variation (CNV) analysis | X | X |
| Detection of translocations and other structural variants | X | X |
| Metagenomic analysis | X | X |
| Bulk RNA-seq (from full-length or fragmented cDNA) | X | X |
| Viral sequencing | X | X |
| cfDNA / ctDNA / liquid biopsy analysis | X | |
| Fragmentomics | X | |
| ChIP-seq | X | |
| Methyl-seq* | X |
*In combination with Equinox Uracil Tolerant Library Amplification Kits.
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