Watchmaker DNA Library Prep Kit with Fragmentation
Accuracy at scale — without the trade-offs.
The Watchmaker DNA Library Prep Kit with Fragmentation brings the scalability and automation of enzymatic shearing to intact genomic DNA, while engineering out the artefacts that usually come with it. False chimeric reads and hairpin-derived false SNVs are the hidden cost of conventional fragmentation chemistries — and they directly undermine sensitive variant calling. This kit suppresses them, so what you sequence is signal, not noise.
One tube, fewer steps, faster.
Combined enzymatic fragmentation, end-repair and A-tailing (FRAG/AT) run in a single reaction, followed by a ready-to-use ligation master mix — cutting hands-on time and producing PCR-free libraries in under 90 minutes. The workflow scales cleanly to high sample numbers and liquid-handling platforms, with generous overages built in.
Tunable by design.
Library size is dialled in through fragmentation time and temperature, delivering consistent inserts across a 5,000-fold input range — from 0.1 ng to 500 ng — and reproducibly between batches. Paired with Equinox® ultra-high-fidelity amplification, the result is even coverage of complex genomes and confident variant detection.
- Artefact-suppressed: up to 90% fewer false chimeric reads and hairpin artefacts than common enzymatic kits.
- High-fidelity: Equinox® amplification cuts overall polymerase error rate by ~40%, including cancer-relevant C>T errors.
- Built for FFPE and low input: robust conversion from degraded and vanishingly small samples, with minimal adapter-dimer.
For Research Use Only. Not for use in diagnostic procedures.
| Parameter | Specification |
| Input range | < 1 ng – 500 ng of intact double-stranded DNA |
| Fragmentation | Enzymatic, tunable by time/temperature (consistent across a 5,000-fold input range) |
| Turnaround time | PCR-free libraries in < 90 minutes |
| Key enzymology | Single-tube FRAG/AT; ready-to-use ligation master mix; Equinox® ultra-high-fidelity amplification |
| Kit contents | Frag/AT Buffer · Frag/AT Enzyme Mix · Ligation Master Mix · Equinox® Library Amplification Master Mix (2X, optional) · P5/P7 Primer Mix (10X, optional) · Full-Length UDI Adapters (optional) |
| Sample compatibility | Intact genomic DNA; high- to low-quality including FFPE |
| PCR-free | Supported for inputs of sufficient mass/quality |
| Sequencing platforms | Illumina; also Element, Singular (G4™), 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 |
| 7K0019-024 / -096 / -384 | Watchmaker DNA Library Prep Kit with Fragmentation — incl. Equinox® Library Amplification Master Mix (2X) and P5/P7 Primer Mix (10X) | 24 / 96 / 384 rxn |
| 7K0013-024 / -096 / -384 | Watchmaker DNA Library Prep Kit with Fragmentation (PCR-free) | 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 + UDI primers |
| FFPE | Compatible; use shorter fragmentation times (start by halving) to match insert sizes from intact DNA |
| Shearing buffer | Mechanical shearing in 10 mM Tris pH 8.0, 0.1 mM EDTA where applicable |
| Tunability | Adjust fragmentation time and temperature to target insert size for read length / application |
| Singular G4™ | Dedicated protocol available with G4™ Universal Adapters |
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Tell us your sample type, input amounts and platform, and we'll help you select and validate the right DNA chemistry — with evaluation samples, automation scripts and local logistics.
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One artefact-suppressed chemistry across DNA applications
Somatic & rare-variant calling
Fewer false chimeras and hairpins mean cleaner structural and SNV calls — critical for low-allele-fraction assays, including FFPE.
Human WGS (incl. PCR-free)
Even coverage of complex genomes and PCR-free libraries in under 90 minutes for high-quality whole-genome data.
WES & targeted capture
Reproducible, tunable inserts make a dependable front end for whole-exome and hybridisation-capture panels.
Inherited disease sequencing
High-fidelity amplification and even coverage support confident germline variant detection.
Single-cell & metagenomics
Robust conversion from low and variable inputs suits single-cell, microbial WGS and metagenomic studies.
Bulk RNA-seq (cDNA input) & viral
Flexible enough for cDNA-input RNA-seq library construction and viral genome sequencing.
Single-tube fragmentation to PCR-free library
Combined steps, no sonicator, ready for automation
1. Frag / AT
Combined enzymatic fragmentation, end-repair and A-tailing in one reaction — tune time and temperature to your target insert.
2. Ligate
A ready-to-use ligation master mix attaches adapters with minimal hands-on time and low adapter-dimer.
3. Go PCR-free or amplify
Finish PCR-free in under 90 minutes, or amplify with Equinox® ultra-high-fidelity master mix.
4. Sequence
Illumina-compatible libraries (also Element, Singular G4™, Ultima) with even coverage of complex genomes.
- ENZYMATIC FRAGMENTATION WITHOUT THE ARTEFACTS
- UP TO 90% FEWER CHIMERAS & HAIRPINS
- ~40% LOWER POLYMERASE ERROR RATE
- TUNABLE INSERTS FROM <1 ng TO 500 ng
- PCR-FREE LIBRARIES IN UNDER 90 MIN
- ENZYMATIC FRAGMENTATION WITHOUT THE ARTEFACTS
- UP TO 90% FEWER CHIMERAS & HAIRPINS
- ~40% LOWER POLYMERASE ERROR RATE
- TUNABLE INSERTS FROM <1 ng TO 500 ng
- PCR-FREE LIBRARIES IN UNDER 90 MIN
Fewer artefacts, truer variants
The hidden cost of enzymatic fragmentation, engineered out
Enzymatic shearing is fast and automatable — but conventional chemistries introduce false chimeric reads and hairpin-derived false SNVs that masquerade as real structural and single-nucleotide variants, especially in low-allele-fraction work. Built from human genomic DNA across 1–200 ng, Watchmaker libraries showed up to a 90% reduction in these artefacts versus two widely used enzymatic kits, approaching the cleanliness of a sonication control without the sample loss or hands-on burden.
Ultra-high-fidelity amplification
~40% lower polymerase error rate where it matters
Even a clean library can be undone by amplification errors that read out as false variants. The Equinox® Library Amplification Master Mix — a proprietary proofreading polymerase — delivered a ~40% reduction in overall error rate versus a widely used high-fidelity HotStart polymerase, with a notable drop in C>T substitutions. That matters: C>T is both a common artefact of cytosine deamination and one of the most frequent true mutation types in cancer, so suppressing it sharpens real-variant confidence.
Tunable shearing across a 5,000-fold input range
Consistent inserts from 0.1 ng to 500 ng
Insert size drives everything downstream — read length, coverage, capture efficiency. This chemistry holds fragment size constant across a 5,000-fold span of input (500 ng to 0.1 ng) under the same conditions, and lets you dial library size precisely through fragmentation time and temperature. It also handles variable sample quality, building efficient libraries from high-quality and formalin-compromised DNA alike — with negligible adapter-dimer even at ultra-low input.
Even coverage, lower sequencing cost
Sequence less to reach the depth you need
Coverage uniformity is quiet but consequential: uneven libraries force you to over-sequence so the worst-covered regions reach target depth. The Watchmaker kit delivers even coverage across complex genomes, reducing the total sequencing — and cost — needed to bring every region of interest to the depth your assay requires.
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 Fragmentation chemistry to your samples and platform.
Use the Fragmentation kit for intact genomic DNA that needs shearing, and for FFPE where enzymatic fragmentation is preferred. Use the Standard kit for already-fragmented inputs such as cfDNA or sonicated DNA.
It is optimised for < 1 ng to 500 ng of intact double-stranded DNA, with consistent fragment sizes maintained across that 5,000-fold range under the same conditions.
Library size is tuned via fragmentation time and temperature. For a given sample quality, a 1 ng and a 500 ng input give the same fragment size under identical conditions.
Yes. Because fixation damage varies, optimise the extraction and shorten the fragmentation time (start by halving) to match the insert sizes achieved with intact DNA.
Yes — PCR-free libraries in under 90 minutes for inputs of sufficient mass and quality. Equinox® amplification is included for workflows that need it.
Combined single-tube chemistry suppresses fragmentation artefacts (chimeras, hairpins) by up to 90%, and Equinox® cuts polymerase error rate by ~40% — together reducing false structural and single-nucleotide calls.
Illumina, Element, Singular (a dedicated G4™ protocol is available) and Ultima; any 3′ T-overhang adapter, including Watchmaker FL-UDI (up to 384-plex) and stubby schemes.
Yes. Watchmaker's quality management system is certified to ISO 13485:2016.