PacBio Onso

Onso is a sequencer released by Pacific Biosciences in April 2023. It is based on Sequencing by Binding (SBB).

PacBio Onso
Photo of Onso: by Illumina

Onso is available in the following models:
  • PromethION with kit 14 chemistry
  • Onso


Manufacturer Pacific Biosciences
Technology Sequencing by Binding (SBB)
Release date April 2023
Price [2] $259,000
MSRP as of March 2024
Type Benchtop
Weight 123 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ
Read length Oxford Nanopore PromethION with kit 14 chemistry: typically 6-20 Kbp
PacBio Onso: 1x200bp to 2x150bp
Run time Oxford Nanopore PromethION with kit 14 chemistry: Up to 72 hours
PacBio Onso: 32-48 hours
Reagent cost per Gb [1] Oxford Nanopore PromethION with kit 14 chemistry: Unavailable
PacBio Onso: Unavailable
Data quality [3] Oxford Nanopore PromethION with kit 14 chemistry: > Q20 (99%) for Simplex reads, ~Q30 (99.9%) for Duplex reads
PacBio Onso: ≥90% Q40+
Maximum output per run (Gb)[4] Oxford Nanopore PromethION with kit 14 chemistry: 13300.00
PacBio Onso: 150.00
Primary error type [5] Substitutions
Notes about the specifications

  1. Cost per Gb: The cost per Gb is calculated by dividing the costs of sequencing reagents by the manufacturer’s maximum output per run. For these runs, the manufacturer may have included their own controls and used specific library preparation kits. Actual performance may vary based on sample and library type and quality, loading concentration, and other experimental factors. The sequencing reagent costs used for calculations do not include any other costs associated with preparing the samples or running the instrument, including reagents used for extraction, quality control or library preparation, labor, electricity, lab consumables, storage, etc. Performance metrics and prices are subject to change.
  2. Price: The final price may be different depending on the supplier, the region and any discounts provided through bulk orders or negotiation. Other factors that may influence the final price are warranty options, maintenance contracts, possible trade-ins of older instruments, and any financing arrangements chosen.
  3. Data quality: This is the maximum data quality that the instrument can offer based on manufacturer’s specifications and optimizations. The quality of a specific run will depend on multiple factors, including sample quality, sample quantity, library prep protocol, run conditions, etc.
  4. Maximum output: This is the maximum output of a full instrument run. This number is based on manufacturer’s specifications and optimizations.
  5. Primary error type: This is the most common type of error that may occur due to sequencing. Other types of error may occur as well.

More about the Onso

The PacBio Onso is a benchtop sequencer targeting the mid-range, short-read next-generation sequencing (NGS) market segment. Launched in 2023, it doesn't have a direct predecessor but competes with established players like Illumina's NextSeq series.

Key Innovations

The Onso's key innovation lies in its use of Sequencing by Binding (SBB) technology, a significant departure from traditional Sequencing by Synthesis (SBS) methods. Unlike SBS, which relies on fluorescently labeled nucleotides for base identification and incorporation in a single step, SBB separates these processes. This separation minimizes chemical modifications to the DNA template strand during sequencing. Fewer modifications translate to fewer errors during base calling, resulting in the Onso's extraordinary accuracy. The system boasts Q40+ base call accuracy, meaning there's a 99.99% chance of a base being called correctly, exceeding most short-read sequencers.

This high accuracy translates into several benefits for researchers. First, it allows for deep variant calling with lower read depth. In standard SBS sequencing, errors introduced during the process can mimic true variations in the DNA sequence. To compensate for this, researchers need to sequence a higher number of reads (increased read depth) to achieve statistically significant variant calls. The Onso's superior accuracy allows researchers to obtain reliable variant calls with lower read depth, ultimately reducing sequencing costs and turnaround times. Additionally, SBB enables detection of low-frequency variants often missed by other platforms. Mutations present in only a small percentage of cells within a sample, such as those found in liquid biopsies or tumor heterogeneity studies, can be obscured by errors in sequencing data. The high fidelity of SBB chemistry makes the Onso ideal for applications demanding detection of rare variants.

Features and Technology

The Onso is a user-friendly, integrated system with a small footprint. It utilizes flow cells with dual lanes and offers 200 and 300 cycle sequencing kits, generating roughly 500 million reads per run.

Another advantage is seamless integration with existing short-read workflows and library preparation methods. Researchers can leverage their established protocols without significant modifications.

Intended Uses and Specific Applications

The Onso's high accuracy makes it suitable for various applications demanding high-fidelity data, including:

  • Targeted panels and whole exomes/genomes: Variant calling and identifying mutations associated with genetic diseases or cancer.
  • Single Cell RNA Sequencing: Studying differential gene expression within single cells with increased confidence in transcript isoforms.
  • Liquid biopsy: Detecting rare cancer mutations circulating in cell-free DNA.

PacBio offers various products to help convert HMW DNA into samples that will be suitable for short-read sequencing, such as the Onso DNA library prep kit. There is also the library conversion kit that enables existing P5/P7 libraries to be sequenced on the Onso.

Comparison with Competing Instruments

  • Illumina NextSeq 550: Offers similar read output and read lengths at shorter run times. However, the NextSeq 550 has lower accuracy than the Onso.
  • Complete Genomics DNBSEQ-G99: This platform has similar read lengths available and much shorter run times. However, it has lower accuracy and lower max output than the Onso.

Special Considerations

Researchers should consider the PacBio Onso if they want to:

  • Prioritize for high-accuracy data: When reliable variant detection or transcript identification is crucial.
  • Focus on cost-effective analysis of lower sample numbers: Due to the potential for reduced sequencing depth with Onso.

Need sequencing done on a PacBio Onso or a specific instrument? Tell us about your project here, and we'll connect you with a qualified provider.

This information on this page is up-to-date as of April 25, 2024 and based on the spec sheets published by the manufacturer.