The Power of Positive
Direct 5mC sequencing for multimodal insights
Traditional methyl-seq workflows convert unmethylated Cs to Ts, which effectively collapses sequence complexity from four bases (ATCG) to three (ATG), limiting utility to methylation analysis. Bisulfite treatment is also highly damaging to DNA, leading to sequence coverage gaps and sample type and mass compatibility limitations.
TAPS+ is a positive-readout chemistry that directly converts methylated Cs (5mCs) to Ts, and preserves unmethylated Cs. This maintains base complexity (ATCG) and delivers 5mC, SNV/indel, and CNV detection from a single library for multimodal analysis across discovery, translational, and population studies, as well as multi-cancer early detection and monitoring applications.
Key Features and Benefits
Table 1. Comparison of methyl-seq methods
- Direct 5mC readout enables simultaneous detection of genetic variants (SNV/Indels and CNVs) and epigenetic modifications from the same library
- Greater than 98% 5mC conversion — including both hypo- and hyper-methylated regions — delivers high true positive and low false positive rates
- Higher sequence diversity boosts mappability, reduces multi-mapping/low-complexity dropouts, and lifts CpG coverage at a given read depth
- Nondamaging workflow delivers robust performance with degraded FFPE and low-input samples (down to 1 ng), including cfDNA
- Streamlined, automation-friendly workflow generates libraries in 6 hours — no columns required
- Reduce computational analysis time by 30% or more, saving hours and associated costs on a 30X genome.
| TAPS+ | EM-Seq | Bisulfite | |
|---|---|---|---|
| Methylation detection accuracy | +++ | +++ | +++ |
| Low false positives | +++ | ++ | ++ |
| Base diversity | +++ | + | + |
| Genomic variant detection | +++ | + | + |
| Non-damaging to DNA with high molecular recovery | +++ | ++ | + |
| Workflow simplicity and automatability | +++ | + | ++ |
| Reduced computational time and costs | +++ | + | + |
Applications
- Methyl sequencing as an alternative to bisulfite conversion, including EPIC arrays
- Whole-genome or targeted methylation sequencing
- Simultaneous detection of methylation, SNV/Indels, and CNVs
- Differential methylation analysis
- Allele-specific methylation analysis
- Multi-cancer early detection (MCED) assay development
- Minimal residual disease (MRD) assay development
- Tumor profiling, including FFPE
- Liquid biopsy (cfDNA/ctDNA) studies
- Fragmentomics
- Aging studies
- Population studies, including epigenome-wide association studies (EWAS)
- Cancer research
- Neurodegenerative research
- Neuroscience and developmental biology
- Biomarker discovery
- Epigenotyping
Preserved base diversity for robust downstream analyses
Figure 1. Sequence a five-base genome. Only ~1–2% of bases in the human genome are cytosines in CpG context, which is where most methylation occurs. TAPS+ converts just those methylated CpG cytosines, leaving the remaining ~20% of cytosines unchanged. The result is a library that preserves native four-base complexity, more closely matches the human genome, and also delivers 5mC detection (the fifth base). This improves alignment and QC metrics, reduces the need for phiX spike-ins, as well as omits the need for costly methylated adapters. It also enables SNV/indel and CNV calling alongside methylation profiling from a single library.
Highly automatable, single-day workflow
Figure 2. Reduce turnaround time with an automatable workflow. The Watchmaker DNA Library Prep Kit with TAPS+ delivers libraries in under 6 hours with a workflow that smoothly translates to automated liquid handlers for high-throughput processing. The method does not require speciality consumables (like conversion columns often used in bisulfite workflows).
*Bisulfite Conversion = EZ DNA Methylation-Gold Kit (Zymo Research) and ssDNA Library Prep = xGen Methyl-Seq Library Prep Kits (IDT)
Key Performance Data
Accurate methylation profiling
By preserving the genome’s native four-base diversity, TAPS+ improves mapping and QC metrics. Its high-efficiency (>98%) 5mC conversion and minimal false positives together enable accurate methylation profiling across both hypo- and hyper-methylated regions.
Accurate methylation profiling
Simultaneously detect methylation and genomic variants
TAPS+ preserves four-base sequence complexity and native coverage profiles, enabling accurate detection of single-nucleotide variants (SNVs) and copy-number variants (CNVs) on-par with an unconverted control. Because SNV and CNV fidelity are maintained alongside direct 5mC readout, a single TAPS+ library supports integrated methylation and variant analysis without compromising performance.
Simultaneously detect methylation and genomic variants
Sensitive methylation and fragmentomic analysis from cfDNA
Methylation signatures in liquid biopsy assays enable sensitive cancer detection, classification, and residual disease monitoring.1,2 TAPS+ preserves cfDNA fragment integrity and delivers high CpG coverage, enabling high-resolution methylation and fragmentomic analysis from low-input samples.
- Vavoulis, D.V., Cutts, A., Thota, N. et al. Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals. Nat Commun 16, 430 (2025)
- Paulina Siejka-Zielińska et al. Cell-free DNA TAPS provides multimodal information for early cancer detection. Sci. Adv. 7,eabh0534(2021).
Sensitive methylation and fragmentomic analysis from cfDNA
Improve data quality and coverage from FFPE samples
TAPS+ preserves DNA integrity from challenging FFPE specimens, enabling simultaneous methylation and variant analysis from a single library. The gentle chemistry improve CpG coverage and reduces false positives and sequence artifacts – enhancing accuracy for tumor-informed and archival studies and expanding the utility of degraded clinically relevant samples.
Improve data quality and coverage from FFPE samples
Reproducible performance enables differential methylation analysis
TAPS+ delivers highly reproducible methylation profiles across technical replicates, with tight CpG-level concordance and stable conversion run to run. In tumor/normal comparisons, it accurately identifies differentially methylated regions (DMRs), capturing both hypo- and hyper-methylation.
Reproducible performance enables differential methylation analysis
Compatible with standard hybrid capture panels for simplified operations
Because TAPS+ preserves the native genome and reads 5mC directly, it’s compatible with standard hybrid-capture panels. This simplifies inventory management and streamlines lab operations.
Compatible with standard hybrid capture panels for simplified operations
BROCHURES
Watchmaker DNA Library Prep with TAPS+ brochure
CNV Calling Liquid Biopsy Methyl Sequencing SNV/SNP/InDel Detection Variant Calling Whole Genome Sequencing Element Illumina Ultima DNA Blood FFPE Frozen Tissue Plasma/cfDNA DNA NGS DNA Library Prep with TAPS+The Watchmaker DNA Library Prep Kit with TAPS+ enables simultaneous detection of methylation and genetic variants from a single library using a gentle, bisulfite-free chemistry. Its streamlined, six-hour workflow preserves DNA integrity and base complexity, delivering high-quality data from 1–200 ng of input - including FFPE and cfDNA samples - for accurate, multimodal genomic and epigenomic analysis.
TECHNICAL LITERATURE
TAPS+ Data Analysis Guide
Methyl Sequencing SNV/SNP/InDel Detection Variant Calling Illumina DNA NGS DNA Library Prep with TAPS+This technical note outlines data analysis approaches for interpreting sequencing data generated with the Watchmaker DNA Library Prep Kit with TAPS+. It compares supported pipelines and tools, highlighting considerations unique to the TAPS+ positive-readout chemistry.
PROTOCOLS
Watchmaker DNA Library Prep with TAPS+ User Guide
Methyl Sequencing DNA DNA NGS DNA Library Prep with TAPS+Protocol for the Watchmaker DNA Library Prep Kit with TAPS+, which enables simultaneous detection of genetic and epigenetic variation from a single library using 1–200 ng of input DNA. The positive-readout chemistry preserves DNA integrity and base complexity from diverse, clinically relevant samples such as FFPE tissue and ctDNA.
| Input range | 1 ng - 200 ng |
|---|---|
| Watchmaker DNA Library Prep Kit (PCR-free) | ER/AT Buffer ER/AT Enzyme Ligation Buffer Ligation Enzyme |
| TAPS+ Kit Methyl-seq | Oxidation Buffer 50 mM DTT Iron (II) Oxidation Cofactor Oxidation Enzyme Stop Solution Reduction Buffer Reduction Reagent Equinox® DHU Tolerant Amplification Master Mix (2X) |
| Optional | P5/P7 Primer Mix (10X) Full-length UDI Adapters |
| Shipping conditions | Ice packs |
| Storage | -20°C ± 5°C |
| Shelf life | (24 rxn): ≥ 6 months (96 rxn): ≥ 6 months |
GENERAL
How does the Watchmaker DNA Library Kit with TAPS+ compare to traditional methylation solutions?
Traditional methods for detecting DNA methylation use bisulfite or enzymes to convert unmethylated cytosines (C) to thymines (T). This reduces nucleotide diversity, making reads harder to align and losing valuable genomic information. Bisulfite treatment can also damage DNA, leaving data gaps. TAPS+ chemistry is a positive readout, directly converting 5-methylcytosine (5mC) to T, which minimizes damage to DNA and retains library and sequence complexity.
What types of modifications does TAPS+ convert?
In the TAPS+ workflow, methylated CpG cytosines — 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) — are converted to a thymine (T) signal during sequencing (a positive readout). Unmethylated CpG cytosines remain C.
What improvements does the Watchmaker DNA Library Prep Kit with TAPS+ offer compared to the original TAPS publication?
TAPS+ builds on the original positive-readout TAPS1 chemistry with a number of improvements:
- Optimized library preparation module that increases sample-to-library conversion for a variety of sample types and improves conversion rates for low-input samples
- Engineered TET enzyme with enhanced activity and stability
- Novel borane reagent
- Specialized DHU amplification module.
All of these elements are refined for real-world samples, allowing for automation and a streamlined, single-day workflow.
- Liu, Y., Siejka-Zielińska, P., Velikova, G. et al. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat Biotechnol 37, 424–429 (2019). https://doi.org/10.1038/s41587-019-0041-2
What is the recommended input range?
The DNA Library Prep Kit with TAPS+ workflow is validated for inputs of 1 - 200 ng.
What are the expected true positive rates?
5-Methylcytosine (5mC) conversion levels and false positive rate may vary by sample type. TAPS+ delivers high true positive rates, converting >98% of 5mC, and low false positives (≤0.3%) with commercially available controls. Contact support@watchmakergenomics.com for more information on commercially available controls and how to assess methylation conversion rates.
What controls are available to determine if my TAPS+ conversion was successful?
Contact support@watchmakergenomics.com for recommended controls to assess conversion and false positive rates. TAPS+ typically results in >98% conversion of 5-Methylcytosine (5mC) and 5-Hydroxymethylcytosine (5hmC) with low (≤ 0.3%) false positives with commercially available controls.
What recommendations do you have for mechanical shearing of DNA?
Mechanical shearing should be carried out in 10 mM Tris pH 8.0, 0.1 mM EDTA. Following shearing, proceed directly into the ER/AT reaction. Do not do a SPRI cleanup between shearing and the ER/AT reaction.
Are there safe stopping points in the workflow?
Yes. There are safe stopping points following ligation, oxidation, and reduction cleanups. These are designated in the user guide along with proper storage conditions.
Is Equinox DHU Tolerant Library Amplification Reagent a hotstart formulation?
Yes. Equinox DHU Tolerant builds on our uracil‑tolerant polymerase, but is specifically developed for TAPS+. The DHU‑Tolerant Library Amplification Master Mix is a hot start, complete formulation engineered for consistent, low GC bias amplification of DHU‑containing templates.
SAMPLE AND REAGENT COMPATIBILITY
What sample types are compatible?
This kit is compatible with multiple sample types, including cell-free DNA, and DNA extracted from blood, cell lines, fresh-frozen tissue, and FFPE samples.
What adapters are compatible?
Unmethylated adapters are required for TAPS+. The Watchmaker DNA Library Prep Kit uses a T/A ligation scheme and is compatible with both truncated (‘stubby’) and full-length adapters. The ligation module is fully compatible with standard UMI adapters and analysis tools. Strand information for methylation analysis is best maintained when using “Y” style adapters.
The Watchmaker DNA Library Prep Kit with TAPS+ is compatible with adapters for a variety of sequencers including those from Illumina, Ultima, Element, and Complete Genomics.
Contact support@watchmakergenomics.com for adapter recommendations.
What SPRI beads are compatible?
AMPure XP beads are required for use with the TAPS+ kit.
What sample buffers are compatible?
DNA in 10 mM Tris pH 8.0, low TE (10 mM Tris pH 8.0, 0.1 mM EDTA) and nuclease free water are suitable sample buffers as input into the ER/AT reaction, the first step in the Watchmaker DNA Library Prep Kit with TAPS+ workflow. Elution buffers for each Ampure XP bead cleanup are specified in the user guide . Use of nuclease free water is required to ensure compatibility with the Oxidation and Reduction steps of the workflow.
SEQUENCING AND ANALYSIS
How should I sequence my libraries?
Final coverage requirements are application and sample specific. Because TAPS+ preserves native base diversity (positive readout), libraries typically run in the same read configuration and with similar efficiency as standard DNA libraries for the same application and platform. In some cases, modestly higher depth may be appropriate based on sample type, input mass, and study goals. PhiX is not required for color balance; follow your instrument vendor guidance and SOPs if a minimal spike-in is standard practice.
What percentage of PhiX is needed for sequencing TAPS+ libraries?
PhiX is not required for sequencing of TAPS+ libraries. The positive methylation readout retains base diversity. Follow your instrument vendor guidance and SOPs if a minimal spike-in is standard practice.
Is the kit compatible with other short read platforms?
Yes. The Watchmaker DNA Library Prep with TAPS+ workflow is compatible with any unmethylated adapters using a T/A ligation scheme.
Element, Ultima, and MGI sequencing chemistries are compatible.
Analysis requirements may differ for single read vs paired read platforms. Contact support@watchmakergenomics.com for our TAPS+ Analysis Recommendations.
Do you have analysis support tools for TAPS+ data?
Yes, we provide open-source support recommendations to help our customers find the optimal analysis solutions for their needs. If you’re comfortable with standard analysis tools like Nextflow and the library of analysis pipelines in nf-core, we’re developing a branch of nf-core/methylseq with TAPS+ support that’s currently under review. For those seeking a more turnkey solution, we recommend exploring the DRAGEN Methylation Pipeline app in Illumina Basespace, and selecting the option to enable TAPS. Contact support@watchmakergenomics.com for a guide to TAPS+ analysis.
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| Description | 24 rxn | 96 rxn | |
|---|---|---|---|
| Watchmaker DNA Library Prep Kit with TAPS+ incl. reagents for DNA library prep, TAPS+ conversion, and amplification | 7BK0003-024 | 7BK0003-096 | Request a quote |
Please contact sales@watchmakergenomics.com to inquire about custom kit configurations.
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