PacBio SMRT Sequencing Technology — HiFi Long-Read Genomics Services at CD Genomics

At a glance:

• The HiFi Advantage
• How PacBio SMRT Sequencing Works
• PacBio Platforms at CD Genomics
• PacBio Services by Research Application
• PacBio vs Other Sequencing Technologies
• Sample Requirements
• Bioinformatics and Data Delivery
• Frequently Asked Questions
• Demo

How PacBio SMRT Sequencing Works — From ZMW to HiFi Read

PacBio SMRT sequencing operates on a principle that is elegantly simple and technically demanding. A single DNA polymerase molecule is immobilized at the bottom of a zero-mode waveguide (ZMW) — a nanophotonic chamber approximately 70 nm in diameter, smaller than the wavelength of visible light. The ZMW creates an observation volume of roughly 20 zeptoliters, confining fluorescence detection to the immediate vicinity of the polymerase active site.

The DNA template is prepared as a SMRTbell — a double-stranded molecule with hairpin adapters ligated to both ends, creating a topologically circular template. When the polymerase begins synthesis, it incorporates fluorescently labeled nucleotides one at a time. Each incorporation event produces a characteristic light pulse as the fluorophore is held in the detection volume for tens of milliseconds before being cleaved and diffusing away. Because each of the four nucleotides carries a distinct fluorophore, the system records nucleotide identity in real time.

The circular SMRTbell structure is what enables HiFi accuracy. After the polymerase completes one pass around the template, it continues around again — and again. A typical HiFi read represents 10–15 passes around the same molecule. The instrument records all passes as a single continuous read; then the CCS algorithm aligns the subreads, identifies the consensus at each position, and outputs a single HiFi read with Q30+ accuracy. Polymerase kinetics — the inter-pulse duration — are also recorded, providing information about base modifications (5mC, 5hmC) that alter polymerase speed.

This direct detection approach avoids the amplification bias inherent to cluster-based sequencing. GC-rich and AT-rich regions are sequenced with the same efficiency as balanced regions, producing uniform coverage across the genome — a critical advantage for whole-genome methylation analysis where bisulfite conversion would otherwise degrade the sample.

PacBio Services by Research Application

This is where you find the exact PacBio service for your project. CD Genomics delivers 40+ application-specific PacBio HiFi sequencing services organized by research area. Each linked service page includes detailed workflows, sample requirements, bioinformatics deliverables, and case studies where applicable.

Human Genomics with Long-Read Sequencing

PacBio HiFi reads resolve medically critical genomic regions — HLA loci, pharmacogenes, repeat expansion disorders — that short reads routinely miss or mis-map.

• Human Leukocyte Antigen (HLA) Typing — Full-length, phased HLA genotyping across all class I and II genes.
• Human Whole Genome Sequencing — 30× HiFi WGS with structural variant calling, haplotype phasing, and methylation detection.
• Human Long-Amplicon Sequencing — Targeted amplicons up to 20 kb for repeat expansion disorders and pharmacogene panels.
• Human Mitochondrial DNA Sequencing — Full-length mtDNA sequencing with heteroplasmy detection down to 1%.
• Human Genome Structural Variation Detection — Comprehensive SV calling from HiFi reads.
• Full-Length TCR/BCR Repertoire Profiling — Complete V(D)J region sequencing for immune repertoire analysis.

Visit our Human Genomics with Long-Read Sequencing hub for all services.

Animal and Plant Genomics with Long-Read Sequencing

Large, repetitive, and polyploid genomes — common in plants and many animals — are where PacBio HiFi demonstrates its most dramatic advantage over short reads. A single HiFi read spans repetitive elements that would fragment an Illumina assembly into hundreds of contigs.

• Animal/Plant Whole Genome Sequencing — Resequencing with HiFi reads for SV detection and allele phasing.
• Animal/Plant Whole Genome De Novo Sequencing — High-contiguity genome assembly achieving chromosome-scale scaffolds.
• Animal/Plant Long Amplicon Sequencing — Targeted long-range PCR products for resistance gene clusters and QTL fine-mapping.
• Animal/Plant RNA Sequencing — Full-length transcript isoform identification in non-model species.
• Pan-Genome Analysis — Multi-sample HiFi assemblies capturing presence/absence variation across populations.
• Mitochondrial/Chloroplast Genome Sequencing — Complete organellar genome assembly without enrichment.
• SSRs/STRs Analysis — Accurate microsatellite genotyping from HiFi reads, avoiding PCR stutter artifacts.
• Haplotype-resolved T2T Genome Assembly — Phased, telomere-to-telomere assemblies resolving both haplotypes.
• T2T Genome Assembly — Complete genome including centromeres, telomeres, and rDNA arrays.

Browse all services in our Animal and Plant Genomics with Long-Read Sequencing hub.

Microbial Genomics with Long-Read Sequencing

HiFi reads enable complete, closed microbial genomes — chromosome(s) plus plasmids — in a single SMRT Cell run. You get a finished genome, not a draft with 50 gaps that need PCR closure.

• Bacterial Whole-Genome Resequencing — Complete circular genomes with plasmid resolution and AMR gene identification.
• Fungal Whole-Genome Resequencing — HiFi WGS for fungal species with large, repeat-rich genomes.
• Viral Whole-Genome Resequencing — Full-length viral genome sequencing, including quasispecies analysis.
• Bacterial Whole-Genome De Novo Sequencing — Complete, closed genome assembly for novel bacterial isolates.
• Fungal Whole-Genome De Novo Sequencing — De novo assembly of fungal genomes with chromosome-level contiguity.
• Viral Genome De Novo Sequencing — Novel virus discovery and complete genome characterization.
• Long-Read Metagenomics Sequencing — Species-level taxonomic resolution from complex communities.
• Full-Length 16S/18S/ITS Amplicon Sequencing — Complete rRNA gene sequencing for strain-level profiling.
• Full-Length Plasmid Sequencing — Complete plasmid characterization.
• Antibiotic Resistance Gene (ARG) Analysis — Comprehensive ARG detection with genomic context from HiFi reads.

See all microbial services at our Microbial Genomics with Long-Read Sequencing hub.

Transcriptomics with Long-Read Sequencing

Short-read RNA-seq counts fragments, not isoforms. PacBio Iso-Seq reads entire transcripts — 5' end to 3' poly(A) tail — in a single HiFi read, revealing the complete isoform landscape.

• Full-Length Transcript Sequencing (Iso-Seq) — Gold-standard PacBio-native method for complete isoform discovery.
• TAIL Iso-Seq — Iso-Seq with poly(A) tail length measurement.
• Single-Cell Full-Length Transcriptome Sequencing — Per-cell isoform expression using MAS-seq.
• circRNA Full-Length Identification and Quantification — Complete circular RNA characterization.
• Poly(A) Tail Length Analysis — Direct measurement of poly(A) tail length distribution.
• Full-Length Transcriptome Profiling — Combined Iso-Seq with short-read quantification.
• Full-Length Spatial-Temporal Transcriptome Profiling — Isoform-level expression across tissues and conditions.

Explore all transcriptomics services at our Transcriptomics with Long-Read Sequencing hub.

Epigenetics and Methylation Analysis Using Long-Read Sequencing

PacBio SMRT sequencing detects 5mC and 5hmC directly from polymerase kinetics — no bisulfite conversion, no antibody enrichment. The same HiFi read delivers both sequence and methylation status.

• Long-Read Sequencing of DNA Methylation — Whole-genome 5mC and 5hmC detection at single-nucleotide resolution.
• Fiber-seq Service — Chromatin fiber analysis for nucleosome positioning and methylation.
• HiFi-C Sequencing Service — Multi-contact 3D genome mapping with methylation detection.

Visit our Epigenetics and Methylation Analysis hub.

Whole-Genome Resequencing with Long-Read Sequencing

When you need population-level variation or causal mutation identification, HiFi captures the full variant spectrum — SNVs, indels, SVs — in one experiment.

• Variant Calling — Comprehensive SNV, indel, and SV detection with haplotype phasing.
• GWAS — HiFi-powered GWAS capturing SV associations missed by SNP arrays.
• Population Evolution — Comparative population genomics leveraging SVs as evolutionary markers.

All resequencing services at Whole-Genome Resequencing.

Pre-Made Library and Data Analysis Services

• PacBio Pre-Made Library Sequencing — Submit prepared SMRTbell libraries for HiFi sequencing on Revio or Vega.
• PacBio Sequencing Data Analysis — Custom bioinformatics: assembly, variant calling, methylation, Iso-Seq analysis.

Visit Pre-Made Library Services and Data Analysis Services.

Sample Requirements for PacBio HiFi Sequencing

PacBio HiFi sequencing performance depends critically on input DNA quality, particularly molecular weight. HiFi reads average 15-25 kb, and the library preparation process with size selection determines the final read length distribution — which starts with the quality of your extracted DNA.

For detailed protocols, shipping instructions, and application-specific requirements, consult our Sample Submission Guideline. Our project managers review every submission and will contact you if additional material or preparation is needed.

Frequently Asked Questions

For research use only. Not for use in diagnostic procedures.