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Arima CiFi Kit

Combine Hi-C and long-read sequencing for complete genome insights.

 

Arima CiFi Kit Overview

Arima CiFi Kit
 

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Short-read sequencing, while well established, leaves critical gaps in repetitive and complex regions — limiting the depth and completeness of your research. The Arima CiFi Kit couples chromosome conformation capture (3C) chemistry with PacBio HiFi long-read sequencing to produce multi-contact reads that resolve chromatin architecture across regions that short-read Hi-C cannot.

Developed and published by McGinty, Kaya et al., Nature Communications 2026, the CiFi method starts from as little as sub-microgram DNA (~60,000 cells) and produces multi-kilobase HiFi reads containing several interacting, concatenated segments (~350 bp to 2 kbp each). The increased read length and multiplicity dramatically improve read-mapping efficiency in repetitive regions and boosted haplotype phasing performance. In head-to-head validation, CiFi delivered 83–89% mapping efficiency in repetitive regions vs. 33–37% for short-read single enzyme Hi-C and improved haplotype phasing to 80.3% vs. 10.9%. The authors also demonstrated chromosome-scale scaffolded assembly from as few as 62,000 cells and from single small insects including a single Anopheles coluzzii mosquito and a Ceratitis capitata Mediterranean fruit fly.

For biology in centromeres, segmental duplications, disease-associated hotspots, low-complexity loci, and small or precious samples, CiFi opens up territory that has been out of reach for short-read Hi-C alone.

Key Features & Benefits

  • One platform, complete data. Integrate chromosome-scale scaffolding, haplotype phasing, and sequencing without separate Hi-C and HiFi runs.
  • Genuinely low input. Sub-microgram DNA / ~60,000 cells; assemblies demonstrated from single insects.
  • Built-in Digestion QC and Ligation QC. Aliquots collected mid-protocol allow direct assessment of restriction efficiency and proximity-ligation efficiency by gel electrophoresis before you commit to sequencing.
  • Flexible sample compatibility. Plants, animals, invertebrates, down to single organisms.
  • Built-in quality assurance. Designed to support reliable, reproducible, publication-quality results.
  • Ready-to-use convenience. 8-reaction kit with an optimized, streamlined protocol.

Arima CiFi is an experimental workflow that captures the sequence and structure (three-dimensional conformation) of genomes. As illustrated in the Arima 3C workflow schematic above, crosslinked chromatin in customer provided crosslinked cells was digested using a single restriction enzyme. Next, spatially proximal digested ends of DNA were ligated. The protein crosslinks are removed and the DNA is purified. Subsequently, this can be followed by size selection to enrich for longer concatemers with multiple proximity contacts. This is followed by Ampli-Fi amplificaiton to amplify 3C concatemers while preserving multi-contact information and then SMRT bell library preparation and sequencing.

How the Arima CiFi Kit Works

How the Arima CiFi Kit Works

 

Arima CiFi Kit Contents

Box Reagents Storage
Box A Stop Solution 1 20–25°C
Conditioning Solution
Stop Solution 2
Buffer D
Buffer E
Elution Buffer
Wash Buffer
Box B Enzyme H2 −20°C
Enzyme C
Enzyme D
Buffer C
Lysis Buffer
Buffer H
Box C Enzyme H1 -80°C



 

Arima CiFi Kit Data

Arima CiFi Kit Chromatin contact maps
(Click image to enlarge)

Figure 1. Chromatin contact maps for GM12878 lymphoblastoid cells across a range of input cell titrations, chromosome 1
Hi-C-style contact matrices for chromosome 1 in the human GM12878 lymphoblastoid cell line (LCL), generated from a titration series of starting cell inputs ranging from 62K to 5M cells (listed left to right, top to bottom). All contacts were normalized using the Knight–Ruiz algorithm and visualized at 250-kb resolution. The 5M condition using the original CiFi protocol serves as a benchmark, matching the input amount used in the initial successful CiFi run. Across the titration series, contact patterns remain consistent, demonstrating that chromatin architecture can be reliably captured even at substantially reduced cell input. Source data are available through NCBI BioProject accession PRJEB83708.

Resource: McGinty, et al. (2025). CiFi: accurate long-read chromosome conformation capture with low-input requirements. Nature Communications, 17(1), 215. https://doi.org/10.1038/s41467-025-66918-y

 

Arima CiFi Kit Genome-wide contact map
(Click image to enlarge)

Figure 2. Genome-wide contact map of the curated prairie vole (Microtus ochrogaster) chromosome-scale assembly, generated using CiFi.
This heatmap displays chromatin contact frequencies across the curated prairie vole genome assembly, generated using CiFi (chromosome conformation capture coupled with PacBio HiFi long-read sequencing), with each axis representing genomic position ordered by chromosome. The strong diagonal signal, organized into discrete square blocks, reflects the expected pattern of chromosome conformation capture data, where each block corresponds to an individual chromosome and confirms proper scaffolding and assembly contiguity. The absence of off-diagonal contacts between blocks indicates minimal misassembly or chromosome-scale scaffolding errors, supporting the high quality of the curated diploid genome achieved using the combined PacBio HiFi and CiFi single-library sequencing strategy.

Resource: Abuelanin, M., et al. (2026). Single-library chromosome-scale diploid assemblies of vole genomes resolve a species-specific duplication implicated in pair bonding. bioRxiv. https://doi.org/10.64898/2026.03.13.711624

 

Arima CiFi Kit Contact Matrices
(Click image to enlarge)

Figure 3. Comparison of chromatin contact maps generated by Hi-C and CiFi at chr2_hap1:92.41–94.36 Mb
Contact matrices for the same genomic region (chr2_hap1, haplotype 1) are shown side by side, generated from Hi-C data (left) andPacBio CiFi long-read data (right), at two bin resolutions: 10 kb (top) and 25 kb (bottom). Color intensity reflects contact frequencybetween genomic bins, with darker red indicating stronger interactions. At both resolutions, CiFi recovers contact patternscomparable to Hi-C, including the characteristic diagonal enrichment and off-diagonal interaction domains, demonstrating that long-read-based chromatin contact mapping can capture chromatin architecture at a level of detail consistent with conventional Hi-C.

 

Arima CiFi Kit FAQs

CiFi (Chromatin conformation capture with HiFi long reads) combines Arima 3C proximity-ligation chemistry with PacBio HiFi long-read sequencing. Unlike standard Hi-C, which typically generates paired-end short reads representing individual chromatin contacts, CiFi produces long HiFi reads containing multiple concatenated interacting genomic segments. This can improve mapping in repetitive genomic regions, support haplotype phasing, and enable 3D genome analysis with lower input requirements.

The CiFi Kit recommends at least 50 mg of fresh-frozen tissue, 1 mL of whole blood, 2.5 g of plant tissue, or more than 1 million cells per sample. Published research has also demonstrated CiFi using substantially lower inputs, including approximately 60,000 cells and individual small insects.

CiFi requires PacBio HiFi long-read sequencing. Recommended sequencing depth depends on the number of samples, genome size, and research applications.

CiFi sequencing requirements depend on the genome size, number of samples, desired interaction resolution, and research application. CiFi libraries are sequenced on PacBio SMRT Cells using HiFi long-read sequencing. Multiple CiFi libraries can be multiplexed on a SMRT Cell, with the number of samples determined by the genome size and desired sequencing depth.

As a general planning example:

  • Small genomes (~100–500 Mb): Multiple samples may be multiplexed on a SMRT Cell because less sequencing data is required per sample.
  • Medium-sized genomes (~1–2.5 Gb): Fewer samples may be multiplexed per SMRT Cell to provide sufficient sequencing depth.
  • uman-sized genomes (~3.1 Gb): More sequencing data is required per sample, so fewer samples may be multiplexed per SMRT Cell compared with smaller genomes.

The appropriate number of PacBio SMRT Cells should be determined based on genome size, number of samples, desired chromatin interaction resolution, and downstream application.

The primary CiFi output is a BAM file. CiFi data can be analyzed using the workflow described by McGinty, Kaya et al. in Nature Communications (2026). The analysis enables identification and characterization of chromatin interactions from long-read sequencing data.

Yes. CiFi pairwise chromatin interactions have shown high concordance with standard Hi-C in a human lymphoblastoid cell line. CiFi can also provide additional advantages for resolving topologically associating domains (TADs) across challenging genomic regions, including centromeres, segmental duplications, and disease-associated genomic hotspots.

CiFi has been demonstrated using human cell lines, individual mosquitoes, individual fruit flies, and plant material. The CiFi workflow is designed for flexible sample compatibility across animal, invertebrate, and plant samples.

Active Motif's current CiFi service availability should be confirmed before submitting a project. CiFi library preparation and PacBio HiFi sequencing may be available as custom project services depending on the current service offering.

The CiFi Kit includes 8 reactions (Cat. No. 53237).

If you need assistance at any time, please call or send an e-mail to Active Motif Technical Service at one of the locations listed below.

North America

Email: [email protected]
Phone: Toll Free - 877 222 9543
Phone: Direct - 760 431 1263
Fax: 760 431 1351

Europe

Email: [email protected]
Phone: Direct: +32 (0)2 653 0001
Fax: +32 (0)2 653 0050

Japan

Email: [email protected]
Phone: +81 (0)3 5225 3638
Fax: +81 (0)3 5261 8733

China

Email: [email protected]
Phone: (86)-21-20926090


 

Arima CiFi Kit Publications

Reference Protocols:

  • McGinty S.P., Kaya G., Sim S.B., Makunin A., Corpuz R.L., Quail M.A., Abuelanin M., Lawniczak M.K.N., Geib S.M., Korlach J., Dennis M.Y. CiFi: accurate long-read chromosome conformation capture with low-input requirements. Nature Communications 17, 215 (2026). https://doi.org/10.1038/s41467-025-66918-y
 

Arima CiFi Kit Documents

 


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