Arima CiFi™

Integrate Hi-C and PacBio HiFi with Arima CiFi™

CiFi™ Kit enables chromatin capture that easily integrates with PacBio HiFi sequencing to better resolve repetitive genomic regions, complete challenging assemblies, and achieve reference-quality genomes from diverse sample types — including low input. Rather than using multiple platforms, you can now generate scaffolding, phasing, and 3D genome data from a single sequencing run.

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Proven Technology

Enhance resolution and genome coverage with trusted Arima Hi-C chemistry combined with proven PacBio accuracy

Streamlined Workflow

Gain research insights quickly with our optimized CiFi protocol and complete reagent kit for efficient library prep and seamless PacBio sequencing

Sample Flexibility

Analyze a variety of sample types including plant, animals and low-input samples

From Sample to Data

With our easy-to-use workflow, you can rapidly go from sample to data.

CiFi Prep

Easy to follow protocol

Compatible with cell lines, primary cells, fresh tissue, and single organisms

Library Prep

Generate high-quality PacBio libraries

Refer to AmpliFi protocol and standard SMRTbell® library preparation workflow

Sequencing

Process on recommended PacBio platform

Coverage and sequencing depth will vary based on project requirements. Contact technical support

Data Analysis

Analyze with suggested protocol

Follow Pore-C workflow described in McGinty publication

Benefits of the Arima CiFi Workflow

One platform, complete data — integrate scaffolding, phasing, and 3D genome data without separate Hi-C and HiFi runs

Flexible sample compatibility — work with plants, animals, invertebrates, or low input samples down to single organisms

Built-in quality assurance—integrated QC checkpoints deliver reliable, reproducible, publication-quality results

Ready-to-use convenience — 8-reaction kit with optimized protocol for fast, efficient setup

From Contigs to Phased Chromosomes in One Platform

The authors developed CiFi and applied it to generate chromosome-scale assemblies and chromatin interaction maps from human cell lines, single mosquitos, and single fruit flies. Key findings include superior mapping in repetitive regions (83-89% vs. 33-37% for short-read Hi-C), improved haplotype phasing (80.3% vs. 10.9%), and successful assembly from as few as 62,000 cells.

McGinty, S.P., Kaya, G., Sim, S.B. et al. CiFi: accurate long-read chromosome conformation capture with low-input requirements. Nat Commun 17, 215 (2026). https://doi.org/10.1038/s41467-025-66918-y

Arima-HiC+ Publications

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Unlock new insights into chromatin architecture with CiFi—a cutting-edge method that combines chromatin conformation capture (3C) and PacBio HiFi long-read sequencing for accurate analysis of complex, repetitive genomic regions from low-input or challenging samples.

CiFi couples chromatin conformation capture (3C) with PacBio HiFi long-read sequencing to produce chromosome-scale, haplotype-resolved genome assemblies and high-resolution chromatin interaction maps from low-input or challenging samples—including single insects—outperforming short-read Hi-C in repetitive regions and haplotype phasing.

Not ready to run CiFi in-house? Let our expert service team handle your complete project—from sample QC and library preparation through PacBio sequencing and bioinformatic analysis

Hear What Our Customers Have to Say

Michael Quail

Principal Scientific Manager of DNA Pipelines, Wellcome Sanger Institute

“The newer Arima kits are being used because we found them to be robust across a range of tissue types from diverse vertebrate and invertebrate species. Kit robustness to a diversity of samples is an essential requirement for the Darwin Tree of Life Project.”