PacBio and UC Davis Researchers Introduce CiFi, a New Long-Read 3C Method That Enables Chromosome-Scale Assemblies from a Single SMRT Cell
Community-developed approach combines multi-contact 3C with HiFi sequencing to deliver haplotype-resolved assemblies from minimal input material
MENLO PARK, Calif., Jan. 08, 2026 (GLOBE NEWSWIRE) -- PacBio (NASDAQ: PACB), developer of the world's most advanced sequencing technologies, today announced CiFi, a new community-developed method that enables chromosome-scale, haplotype-resolved genome assemblies from a single sequencing run, even when sample material is limited. By integrating chromatin conformation capture (3C) with PacBio HiFi long-read sequencing, CiFi delivers multi-contact reads and longer fragments that significantly increase the information content of proximity ligation experiments in a single Revio sequencing run.
A defining by researchers in the Megan Dennis Laboratory at the University of California, Davis, shows how CiFi addresses long-standing limitations of short-read Hi-C by generating long, highly accurate reads that capture multiple chromatin interactions within a single molecule. The new method offers several advantages tailored to the needs of genome biology, biodiversity studies, and functional genomics.
These include improved mapping in repetitive regions, removing obstacles around low input performance, enabling multi-contact resolution, and saving project time and complexity through single platform simplicity.
“CiFi expands our multiomics capabilities, increasing what we can do on HiFi sequencing systems without new hardware and unlocking new customer use cases,” said David Miller, Vice President of Global Marketing at PacBio. “The work from the Megan Dennis Lab at UC Davis shows what becomes possible when innovative chromatin capture methods are paired with the accuracy of HiFi sequencing.”
When paired with Revio SPRQ chemistry, CiFi makes it possible to generate reference-quality assemblies using fewer cells, fewer libraries, and fewer sequencing runs. This lowers barriers for genome projects that have been limited by cost, complexity, or sample availability.
Traditional Hi-C approaches typically capture only two interacting genomic fragments per read pair and often struggle in repetitive or structurally complex regions. CiFi overcomes these limitations by producing long, concatemeric HiFi reads that can contain many interacting chromatin fragments, substantially increasing contact density while maintaining the accuracy of PacBio HiFi sequencing.
"We developed CiFi to make high-accuracy, multi-contact chromatin capture accessible to researchers working with limited or challenging samples,” said Megan Dennis, PhD, Associate Professor at UC Davis. “By combining 3C with HiFi sequencing, we can resolve chromatin architecture across complex genomic regions and generate chromosome-scale assemblies with greater confidence and far less input.”
In a demonstration of the method’s capabilities, UC Davis and PacBio applied the CiFi developed workflow to the prairie and meadow vole. The resulting uncurated assemblies achieved scaffold N50 values exceeding one hundred million base pairs, with telomeric sequence detected at both ends of many scaffolds. These results show that the UC Davis developed CiFi method, combined with HiFi sequencing, can routinely deliver chromosome scale, reference quality assemblies using only one sequencing run.
For more information about CiFi, visit the Application Note .
About PacBio
PacBio (NASDAQ: PACB) is a premier life science technology company that designs, develops, and manufactures advanced sequencing solutions to help scientists and clinical researchers resolve genetically complex problems. Our products and technologies, which include our HiFi long-read sequencing, address solutions across a broad set of research applications including human germline sequencing, plant and animal sciences, infectious disease and microbiology, oncology, and other emerging applications. For more information, please visit and follow @PacBio.
PacBio products are provided for Research Use Only. Not for use in diagnostic procedures.
Forward Looking Statements
This press release may contain “forward-looking statements” within the meaning of Section 21E of the Securities Exchange Act of 1934, as amended, and the U.S. Private Securities Litigation Reform Act of 1995. All statements other than statements of historical fact are forward-looking statements, including statements relating to: the uses, advantages, or quality or performance of, or benefits or expected benefits of using, PacBio products or technologies, such as in connection with genome biology, biodiversity studies, and functional genomics, improved mapping in repetitive regions, removing obstacles around low input performance, enabling multi-contact resolution, saving project time and complexity, expanding multiomics capabilities, generating reference-quality assemblies with fewer cells, libraries and sequencing runs, resolving chromatin architecture with less input, and other future events. You should not place undue reliance on forward-looking statements because they are subject to assumptions, risks, and uncertainties and could cause actual outcomes and results to differ materially from currently anticipated results, including, challenges inherent in using new sequencing methods, the difficulty of generating discoveries in new areas of research; potential product performance and quality issues; third-party claims alleging infringement of patents and proprietary rights or seeking to invalidate PacBio's patents or proprietary rights, among others. Additional factors that could materially affect actual results can be found in PacBio's most recent filings with the Securities and Exchange Commission, including PacBio's most recent reports on Forms 8-K, 10-K, and 10-Q, and include those listed under the caption "Risk Factors." These forward-looking statements are based on current expectations and speak only as of the date hereof; except as required by law, PacBio disclaims any obligation to revise or update these forward-looking statements to reflect events or circumstances in the future, even if new information becomes available.
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