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Precision Engineered. Tailored to Your Workflow: Find Your Watchmaker Genomics Solution.
At Sopachem, we understand that high-quality sequencing data begins long before the sequencer runs. As the official distributor of Watchmaker Genomics, we are proud to offer their complete, cutting-edge portfolio of next-generation sequencing (NGS) library preparation reagents and enzyme configurations.
Watchmaker Genomics specializes in the intersection of enzyme engineering and high-throughput genomics. By rewriting the standards for enzyme performance, they address the most persistent bottlenecks in sequencing workflows—such as bias, low conversion efficiency, and artifact generation. Whether you are working with challenging, low-input samples like FFPE tissue, or running high-throughput clinical assays, Watchmaker’s solutions deliver the ultimate combination of speed, fidelity, and yield.
Find Your Perfect Configuration
Because no two genomic applications are identical, Watchmaker’s solutions are highly versatile. This solution page is designed to act as your interactive guide. Below, you can explore the entire portfolio and determine exactly which kit, enzyme mix, and specific configuration is optimized to meet the unique demands of your application.
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Whether you need advice on challenging low-input/FFPE samples or want to integrate Watchmaker Genomics enzymes into your current protocol, we’re here to help. Get in touch for custom advice and technical support.
cfDNA/ctDNA
Oncology Assays & Liquid Biopsies
To reliably catch ultra-low frequency somatic mutations and copy number variations from limited, highly precious liquid biopsy samples without losing rare variant data to sequencing noise or background bias.
Watchmaker DNA Library Prep Kit (Without Fragmentation) | ||
| 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. | ||
| Recommended Custom Components |
| Full-Length Unique Dual-Index (UDI) Adapters (for PCR-free workflows or low-frequency variant filtering). |
| Maximize Every Microliter |
| Cell-free DNA is scarce and pre-fragmented. Watchmaker’s specialized, single-tube ligation chemistry exhibits industry-leading conversion efficiency, turning significantly more of your raw cfDNA fragments into sequenceable libraries compared to standard commercial kits. |
| Suppressed Background Artifacts |
| When searching for <0.1% allele frequencies, background errors can mimic actual tumor mutations. This configuration minimizes artificial sequence alterations, ensuring that your low-frequency variant detection is clean, true, and highly reproducible. |
| PCR-Free Compatibility |
| Thanks to high initial conversion yields, you can completely bypass library amplification for many cfDNA setups, removing PCR-introduced duplication bottlenecks entirely. |
FFPE
Challenging & Degraded Samples
To unlock high-complexity, low-bias libraries from heavily damaged biobank or clinical tissues while suppressing false-positive mutations caused by chemical cross-linking and storage artifacts.
Watchmaker DNA Library Prep Kit with Fragmentation | ||
| 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. | ||
| Recommended Custom Components: | ||
| Custom Fragmentation Time Profiles (tuned specifically to your tissue's baseline degradation level). | ||
| Suppression of Artifact Errors |
| FFPE fixation creates artificial sequence variants (artifacts) that look like true somatic mutations. Watchmaker’s integrated FFPE repair chemistry actively treats this damage during the workflow, preventing the propagation of false-positive data. |
| Gentle, Uniform Fragmentation |
| Traditional mechanical shearing destroys fragile, degraded templates. Watchmaker’s specialized, tunable enzymatic fragmentation splits genomic DNA precisely and uniformly without introducing sequence bias or artificial chimeric loops. |
| Maximize Library Complexity |
| By combining fragmentation, end-repair, and A-tailing into a single, seamless reaction tube, sample-handling loss can be virtually eliminated, guaranteeing high conversion rates from ultra-low mass clinical tissue. |
WGS & WES
Whole Genome & Whole Exome Sequencing
To achieve complete, ultra-uniform genome coverage across both highly challenging AT- and GC-rich regions, while maximizing sequencing economics and reducing the need for costly over-sequencing.
Watchmaker DNA Library Prep Kit with Fragmentation | ||
| 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. | ||
| Recommended Custom Components: |
| Equinox Library Amplification Kit |
| Flawless Uniformity, Lower Costs |
| High-throughput WGS economics depend heavily on uniform coverage. Watchmaker’s library prep paired with the Equinox Master Mix ensures that difficult genomic regions amplify equally, eliminating "dead zones" and preventing unnecesssary over-sequencing. |
| True PCR-Free Performance |
| Thanks to industry-leading initial ligation yields, labs can completely bypass library amplification for high-mass inputs, removing PCR-introduced duplication bottlenecks entirely. |
| Automation-Ready Scale |
| This chemistry features flexible, robust incubation tolerances and stable master mixes designed to drop straight into automated high-throughput liquid handling platforms. Buffer overage and optimized liquid characteristics help automation even more. |
Hybridization Capture
Targeted Sequencing
To generate highly complex, robust starting libraries that maximize on-target capture efficiency and multiplexing capabilities for custom panels and exome designs.
Watchmaker DNA Library Prep Kit | ||
| 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. | ||
| Recommended Custom Components: |
| Equinox High Concentration (HC) Library Amplification Kit (4X) |
| Unmatched Library Density |
| Hybridization capture success relies on the raw molecular complexity of your input library. Watchmaker delivers an exceptionally high library conversion rate, giving your capture probes more unique molecules to bind to. |
| Flexible Automation Footprint |
| The Equinox HC (4X concentrated) master mix allows for flexible reaction volume adjustments, allowing high-throughput core labs to scale down reaction sizes and fit within tight liquid handler parameters. |
| Minimal Duplication Rates |
| The ultra-efficient fidelity of the Equinox amplification system means you can achieve the necessary library yields for capture panels using fewer PCR cycles, keeping duplication rates at an absolute minimum. |
WTS
Whole Transcriptome Sequencing
Deep, stranded interrogation of both coding and non-coding RNA profiles from precious, low-input, or highly fragmented tissue samples without losing transcript resolution.
| Watchmaker RNA Library Prep Kit | ||
| Article Number | Description | Reactions |
| 7K0078-024 | Watchmaker RNA Library Prep Kit — incl. reagents for RNA library prep and amplification | 24 rxn |
| 7K0078-096 | Watchmaker RNA Library Prep Kit — incl. reagents for RNA library prep and amplification | 96 rxn |
| 7K0078-384 | Watchmaker RNA Library Prep Kit — incl. reagents for RNA library prep and amplification | 384 rxn |
| Custom fills, concentrations and private-label formats available on request. | ||
| Recommended Custom Components: |
| Unique Dual-Index (UDI) Plate Adapters. |
| Engineered StellarScript RT |
| Standard wild-type reverse transcriptases fail on degraded or low-mass templates. This configuration features an engineered reverse transcriptase that maximizes cDNA conversion efficiency from fragmented FFPE or clinical tissue. |
| Rapid, Single-Day Processing |
| Go from raw extracted RNA to fully prepared, sequence-ready libraries in under 3.5 hours, drastically reducing your turnaround times. |
| Accurate Strand Specificity |
| Retains high strand-directionality information, allowing researchers to accurately map antisense transcripts, novel long non-coding RNAs (lncRNAs), and complex fusion genes. |
Stranded mRNA-Seq
Gene Expression Profiling
Streamlined, cost-effective differential gene expression analysis and biomarker discovery from intact total RNA with high sensitivity for low-abundance transcripts.
| Watchmaker mRNA Library Prep Kit | ||
| Article Number | Description | Reactions |
| 7BK0001-024 | Watchmaker mRNA Library Prep Kit — incl. reagents for mRNA capture, RNA library prep and amplification | 24 rxn |
| 7BK0001-096 | Watchmaker mRNA Library Prep Kit — incl. reagents for mRNA capture, RNA library prep and amplification | 96 rxn |
| 7BK0001-384 | Watchmaker mRNA Library Prep Kit — incl. reagents for mRNA capture, RNA library prep and amplification | 384 rxn |
| The mRNA Library Prep Kit (7BK0001) ships as two boxes: the mRNA Capture Kit (7K0105) and the RNA Library Prep Kit (7K0078). Custom fills, concentrations and private-label formats are available on request. | ||
| Recommended Custom Components: |
| Integrated Poly(A) Selection Magnetic Beads. |
| Built for High-Throughput Automation |
| This workflow uses on-magnet washes to dramatically reduce hands-on time, sample transfer steps, and pipette tip usage, making it simple to implement on liquid handlers and scale up. |
| Deep Sensitivity for Low Inputs |
| While traditional mRNA kits require microgram inputs, Watchmaker’s high conversion efficiency allows users to reliably map transcripts down to an ultra-sensitive bottom input limit of just 2.5 ng of total RNA. |
| Crisp Dynamic Range |
| Delivers highly accurate transcript quantification, successfully capturing rare, lowly expressed genes without over-saturating the data with high-abundance household genes. |
Whole Blood/FFPE RNA
Ribosomal RNA & Globin Depletion
To cleanly eliminate uninformative ribosomal and globin transcripts from whole blood or degraded tissue RNA, freeing up maximal sequencing depth for relevant biological data.
| Watchmaker RNA Library Prep Kit with Polaris™ Depletion | ||
| Article Number | Description | Reactions |
| 7BK0002-024 | Watchmaker RNA Library Prep Kit with Polaris® Depletion — incl. reagents for rRNA and globin depletion, RNA library prep and amplification | 24 rxn |
| 7BK0002-096 | Watchmaker RNA Library Prep Kit with Polaris® Depletion — incl. reagents for rRNA and globin depletion, RNA library prep and amplification | 96 rxn |
| 7BK0002-384 | Watchmaker RNA Library Prep Kit with Polaris® Depletion — incl. reagents for rRNA and globin depletion, RNA library prep and amplification | 384 rxn |
| Custom fills, concentrations, packaging and private-label formats are available on request. All Polaris probes are based on human, mouse and rat sequences. | ||
| Recommended Custom Components: |
| Specialized Polaris Depletion Probe Panels. |
| Reclaim Your Sequencing Space |
| Ribosomal and globin RNA make up over 90% of total RNA in whole blood and biobank tissue. Watchmaker's Polaris chemistry targets and clears these sequences, reallocating precious sequencing reads back to the informative transcriptome. |
| Ultra-Fast Integrated Workflow |
| Rather than running a separate, clunky depletion assay before starting library prep, Polaris chemistry integrates directly into a rapid, single-day workflow taking less than 4.5 hours total. |
| High Performance on Broken Material |
| Unlike traditional bead-capture depletion which fails on fragmented material, Polaris works enzymatically, effectively destroying targeted uninformative fragments even in highly degraded FFPE-derived RNA. |
Methyl-Seq / TAPS+
DNA Methylation Analysis
Simultaneous, non-destructive profiling of genetic variants and true cytosine methylation (5mC/5hmC) patterns from scarce, low-mass samples without the severe chemical degradation caused by traditional methods.
| Watchmaker DNA Library Prep Kit with TAPS+ | ||
| Article Number | Description | Reactions |
| 7BK0003-024 | Watchmaker DNA Library Prep Kit with TAPS+ — incl. reagents for DNA library prep, TAPS+ conversion and amplification | 24 rxn |
| 7BK0003-096 | Watchmaker DNA Library Prep Kit with TAPS+ — incl. reagents for DNA library prep, TAPS+ conversion and amplification | 96 rxn |
| No 384-rxn format listed. Custom configurations available on request. | ||
| Recommended Custom Components: |
| Equinox Uracil-Tolerant Library Amplification Kit |
| Gentle, Non-Destructive Chemistry |
| Traditional bisulfite treatments destroy up to 90% of your sample DNA using harsh acids. The advanced TAPS+ workflow utilizes mild enzymatic conversion to preserve template structures completely. More complex DNA provides more sequencing information. |
| Unlock cfDNA Epigenomics |
| Because the template remains undamaged, this application unlocks comprehensive methylation sequencing from precious, low-input samples like circulating cell-free DNA (cfDNA), which was previously impossible with bisulfite methods. |
| Uracil-Tolerant High Fidelity |
| Paired with the Equinox Uracil-Tolerant Mix, modified bases are amplified uniformly and without bias, maintaining true library complexity and saving on sequencing depth. |
PCR/Pooling
High-Fidelity Library Amplification & Normalization
To eliminate core-lab operational bottlenecks by achieving error-free library amplification alongside automated, mass-action sample normalization without manual quantification steps.
| Equinox Prime Library Amplification Kit | |
| Article Number | Description |
| 7K0014-024 / -096 / -384 | Equinox® Library Amplification Kit — incl. P5/P7 Primer Mix (10X) |
| 7K0021-024 / -096 / -384 | Equinox® Library Amplification Kit — w/o primers |
| 7K0094-096 / -384 | Equinox® HC Library Amplification Kit — incl. P5/P7 Primer Mix (10X) |
| 7K0065-096 / -384 | Equinox® HC Library Amplification Kit — w/o primers |
| 7K0023-024 / -096 / -384 | Equinox® Uracil-Tolerant Amplification Kit — incl. P5/P7 Primer Mix (10X) |
| 7K0028-024 / -096 / -384 | Equinox® Uracil-Tolerant Amplification Kit — w/o primers |
| Non-hot-start formulations and custom fills/labels available on request. Equinox HC is not offered in a 24-rxn size. | |
| Recommended Custom Components: |
| EquiPlex™ Normalization Kit |
| Eliminate Indel and Slippage Errors |
| Equinox Prime is an ultra-fidelity polymerase designed to prevent enzymatic slippage across tricky homopolymer stretches and highly repetitive target sections, dropping background sequencing errors significantly. |
| Quantification-Free Pooling |
| Traditional library pooling requires tedious, manual Qubit or qPCR quantification for every sample. The EquiPlex system uses a unique CRISPR-Cas9-based stoichiometric binding mechanism to seamlessly normalize and pool unequal libraries into a single tube simultaneously. |
| Massive Core Facility Cost Savings |
| By replacing individual sample quantification and manual calculations with a streamlined, batch-pooling assay, core labs can reduce hands-on labor and consumable expenses by up to 70%. |
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