Watchmaker DNA Library Prep Kit (Standard)
Cover your bases — from the most demanding samples.
The Watchmaker DNA Library Prep Kit is engineered to do one thing exceptionally well: convert as much of your template DNA as possible into sequenceable library molecules. For naturally fragmented inputs like cell-free DNA, that efficiency is the difference between a confident call and a missed variant — higher conversion means higher library complexity, deeper coverage and better sequencing economy from precious material.
Designed for ligation efficiency, not just throughput.
The kit takes fragmented double-stranded DNA — cfDNA, mechanically (Covaris®) or enzymatically sheared DNA, and PCR products in the ~150–500 bp range — and builds Illumina-compatible libraries from as little as 500 pg and up to 1 µg. Minimal sample loss, negligible adapter-dimer, low bias and low artefact rates make it a dependable front end for liquid biopsy, hybrid-capture panels and UMI-based assays.
One streamlined run, ready for the deck.
Libraries assemble in under two hours through a simple end-repair/A-tailing and ligation workflow with a built-in safe stopping point. Generous overages on the 96-reaction format suit liquid handlers, and the kit supports PCR-free workflows where input mass and quality allow.
- Liquid-biopsy first: maximises conversion of low-input cfDNA/ctDNA for sensitive, low-frequency variant detection.
- Flexible adapters: compatible with Watchmaker Full-Length UDI Adapters (up to 384-plex) and stubby adapter/UDI primer schemes.
- Methyl-ready: pairs with Equinox® Uracil-Tolerant amplification for methyl-seq, and is the library module behind Watchmaker TAPS+.
For Research Use Only. Not for use in diagnostic procedures.
| Parameter | Specification |
| Input range | 500 pg – 1 µg of fragmented double-stranded DNA (0.5–1000 ng) |
| Input types | cfDNA, mechanically/enzymatically sheared DNA, plasmid DNA, long PCR products |
| Supported fragment length | ~150 – 500 bp |
| Turnaround time | < 2 hours |
| Key enzymology | ER/AT and ligation modules; Equinox® high-fidelity amplification |
| Kit contents | ER/AT Buffer · ER/AT Enzyme · Ligation Buffer · Ligation Enzyme · Equinox® Amplification Master Mix (2X, optional) · P5/P7 Primer Mix (10X, optional) · Full-Length UDI Adapters (optional) |
| Sample compatibility | cfDNA, FFPE (already fragmented), ChIP material; high- to low-quality DNA |
| PCR-free | Supported for inputs of sufficient mass/quality |
| Sequencing platforms | Illumina; also Element, Singular, Ultima |
| Shipping conditions | Ice packs |
| Storage | −20 °C ± 5 °C |
| Shelf life | 24-rxn: ≥ 6 months · > 24-rxn: ≥ 12 months |
| Quality system | Manufactured under ISO 13485:2016 |
| Article Number | Description | Reactions |
| 7K0102-024 / -096 / -384 | Watchmaker DNA Library Prep Kit — incl. Equinox® Library Amplification Master Mix (2X) and P5/P7 Primer Mix (10X) | 24 / 96 / 384 rxn |
| 7K0101-024 / -096 / -384 | Watchmaker DNA Library Prep Kit (PCR-free) | 24 / 96 / 384 rxn |
| 7K0103-024 / -096 / -384 | Watchmaker DNA Library Prep Kit (w/o primers) — incl. Equinox® Library Amplification Master Mix (2X) | 24 / 96 / 384 rxn |
| Full-Length UDI Adapters and stubby adapter/UDI primers are ordered separately. Custom fills, concentrations and private-label formats available on request. | ||
| Topic | Detail |
| Adapters | Any adapter with a 3′ T-overhang — Watchmaker FL-UDI (up to 384-plex) or stubby adapter + UDI primers (e.g. IDT xGen) |
| Quantitation | Quantitate post-fragmentation/purification, ideally by fluorometric method (Qubit / PicoGreen) |
| Methyl-seq | Compatible when amplified with Equinox® Uracil-Tolerant kits; also the library module used by TAPS+ |
| Safe stopping point | After adapter-ligation SPRI clean-up (4 °C up to 1 week, −20 °C up to 1 month) |
| FFPE | Compatible; conversion may be lower/variable. For FFPE needing shearing, use the Fragmentation kit |
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A conversion-first chemistry for fragmented and low-input DNA
cfDNA & ctDNA (liquid biopsy)
Maximises conversion of naturally fragmented cell-free DNA for sensitive, low-frequency variant detection from minimal input.
Somatic & rare-variant calling
Higher library complexity translates to deeper coverage and reliable detection of sub-1% allele fractions.
FFPE (pre-fragmented)
Strong workflow and performance advantages for FFPE that is already fragmented or sonicated.
ChIP-seq
Efficient library construction from limited chromatin-immunoprecipitated material.
WGS, WES & targeted
Supports human WGS (including PCR-free), whole-exome and hybridisation-capture panels across 15–85% GC content.
Methyl-seq & multimodal
The library module for methyl workflows — pairs with Equinox® Uracil-Tolerant amplification and underpins Watchmaker TAPS+
A two-hour, automation-ready workflow
Fewer steps, less sample loss, ready for liquid handlers
1. End repair & A-tail
A single ER/AT reaction prepares fragmented inputs efficiently, with vortex-robust consistency between samples.
2. Ligate
High-efficiency adapter ligation minimises sample loss and adapter-dimer; a safe stopping point follows clean-up.
3. (Optional) amplify
Equinox® high-fidelity master mix delivers low-bias amplification — or run PCR-free where input allows.
4. Sequence
Illumina-compatible libraries (also Element, Singular, Ultima) ready for direct or targeted sequencing.
- MAXIMUM CONVERSION OF cfDNA INTO LIBRARY
- HIGH-COMPLEXITY LIBRARIES FROM 500 pg
- LIBRARIES IN UNDER 2 HOURS
- NEGLIGIBLE ADAPTER-DIMER
- PCR-FREE & AUTOMATION-READY
- MAXIMUM CONVERSION OF cfDNA INTO LIBRARY
- HIGH-COMPLEXITY LIBRARIES FROM 500 pg
- LIBRARIES IN UNDER 2 HOURS
- NEGLIGIBLE ADAPTER-DIMER
- PCR-FREE & AUTOMATION-READY
Convert more cfDNA into signal
Higher yield and coverage from limited liquid-biopsy inputs
Cell-free DNA is a powerful, non-invasive window into oncology, prenatal and transplant biology — but only if enough of it survives library prep. Built from 1 ng of cfDNA, Watchmaker libraries delivered up to 9× higher yield than comparator kits with no adapter-dimer, and 20–30% higher mean deduplicated coverage across a custom oncology panel. More of your sample becomes informative, mappable sequence.
Deeper, more sensitive variant calling
The depth low-frequency variants demand
Liquid-biopsy assays must call variants present at ~0.1% from tiny inputs — which requires real depth at every position of interest. Higher cfDNA conversion gave Watchmaker libraries a 3.5× improvement in the proportion of bases covered at ≥3,000X (the modelled minimum to call 0.1% variants), and all expected variants were detected across replicates. Better sensitivity, and better sequencing economy, from the same reads.
Salvage coverage from FFPE
More usable data from variable-quality archival DNA
FFPE remains the backbone of clinical-research cohorts, yet its variable quality and limited inputs defeat many workflows. For FFPE that is already fragmented — or where sonication is preferred — the Watchmaker kit delivered 10–50% higher coverage than comparator kits, with the largest gains on the low- and medium-quality samples that need help most. (For FFPE requiring shearing, choose the Fragmentation kit.)
Choose the right Watchmaker DNA chemistry
Three DNA chemistries — matched to your sample and question
DNA Library Prep with TAPS+
Direct 5mC methyl-seq plus SNV/Indel/CNV from one library; gentle, bisulfite-free chemistry for FFPE and cfDNA (1–200 ng).
DNA Library Prep Kit (Standard)
For pre-fragmented inputs — cfDNA, sonicated or enzymatically sheared DNA. Maximum conversion for liquid biopsy and low-frequency variants.
DNA Library Prep with Fragmentation
For intact genomic DNA. Tunable enzymatic shearing (<1 ng–500 ng), up to 90% fewer artefacts, PCR-free libraries in <90 min.
COMPLETE YOUR NGS PIPELINE
Tailored Solutions for Challenging Applications
A great result relies on more than just a single high-quality reagent. Visit our Solutions page to see how we integrate cutting-edge technologies, like Watchmaker Genomics, into end-to-end workflows designed to maximize your laboratory’s efficiency and sequencing yield.
Technical insights & kit selection
Practical guidance on matching the DNA chemistry to your samples and platform.
Use the Standard DNA Library Prep Kit for pre-fragmented inputs — cfDNA/ctDNA or DNA already sheared by sonication. For intact genomic DNA (or FFPE needing shearing), use the DNA Library Prep Kit with Fragmentation. For methylation, use TAPS+.
500 pg to 1 µg of fragmented double-stranded DNA, ideally in the ~150–500 bp range. Inputs include cfDNA, mechanically/enzymatically sheared DNA, plasmid DNA and long PCR products.
Yes, for FFPE that is already fragmented. Conversion efficiency can be lower and more variable depending on fixation, storage and extraction. If the FFPE DNA needs shearing, use the Fragmentation kit.
Any adapter with a 3′ T-overhang. Watchmaker Full-Length UDI Adapters enable ligation-based indexing up to 384-plex (and PCR-free use); stubby adapter + UDI primer schemes (e.g. IDT xGen) are also supported.
Yes, for inputs of sufficient mass and quality. The kit also includes Equinox® high-fidelity amplification for workflows where amplification is required; low-input or stubby-adapter libraries need amplification before qPCR/sequencing.
Yes. It prepares dU-containing libraries when amplified with a Watchmaker Equinox® Uracil-Tolerant kit, and it is the library module behind Watchmaker DNA Library Prep with TAPS+.
Yes. The streamlined single-tube-style workflow with generous overages suits liquid handlers; an application note is available for the Revvity Sciclone® G3 NGSx.
Yes. Watchmaker's quality management system is certified to ISO 13485:2016.