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CiFi — PacBio + UC Davis

At a glance

  • Vendor: PacBio (in collaboration with UC Davis; Megan Dennis lab)
  • Launch date / venue: Announced 2026-01-08 (pre-AGBT); featured at AGBT 2026
  • Availability: Shipping (reagent-only protocol) per PacBio CiFi press release, 2026-01-08
  • Modality: Long-read 3C / Hi-C variant on Revio (HiFi reads)
  • Output: Chromosome-scale de novo assembly from 1 SMRT cell per PacBio CiFi PR (vendor PR — no independent benchmark)
  • Accuracy: HiFi base accuracy retained, Q≥30 per base per PacBio CiFi PR
  • Price: Reagent-only (consumes existing Revio SMRT cell footprint)

What's new

CiFi captures 3D chromatin proximity ligations (like Hi-C) but reads them on Revio as HiFi long reads rather than on a short-read sequencer. The combination of HiFi base accuracy and proximity signal collapses what historically required separate HiFi + short-read Hi-C runs into a single SMRT cell run, dropping chromosome-scale assembly cost and turnaround for non-model organism genomics.

Headline benchmarks

  • Chromosome-scale assembly of human and selected non-human references from a single SMRT cell — disclosed in the PacBio/UC Davis announcement; independent N50 / haplotype-resolution metrics from non-UC-Davis groups not yet published as of AGBT per PacBio CiFi PR (vendor PR — no independent benchmark).

Reception / competitive context

CiFi targets the de novo / pangenome / conservation genomics segment where Hi-C scaffolding is mandatory. By eliminating the short-read Hi-C arm, it tightens PacBio's grip on the chromosome-scale-assembly workflow and complements SPRQ-Hq's per-genome economics for population-scale long-read.

  • Companion chemistry: SPRQ-Hq / SMRT-cell reuse (CiFi runs on this chemistry).
  • Downstream Bioconductor: BSgenome and GenomicRanges consume chromosome-scale assemblies for reference packaging and coordinate operations.
  • AGBT 2026 plenary cross-ref: Megan Dennis (UC Davis) on Day 2 AI-in-Genomics plenary.

Sources