PacBio Sequel II

Sequel II is a sequencer released by Pacific Biosciences in December 2020. It is based on Single Molecule Real Time (SMRT) Sequencing.

PacBio Sequel II
Photo of Sequel IIe: by Pacific Biosciences


Manufacturer Pacific Biosciences
Technology Single Molecule Real Time (SMRT) Sequencing
Release date December 2020
Price [2] $495,000
MSRP as of 2020
Type Industrial
Weight 362 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format BAM
Read length PacBio Sequel II: 1x20000bp
Run time PacBio Sequel II: Up to 30 hours
Reagent cost per Gb [1] PacBio Sequel II: Unavailable
Data quality [3] PacBio Sequel II: Up to 4,000,000 HiFi reads >99% accuracy
Maximum output per run (Gb)[4] PacBio Sequel II: 30.00
Primary error type [5] Indels
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 Sequel II

The PacBio Sequel II is a next-generation sequencing (NGS) platform released in 2020 targeting researchers requiring high-fidelity, long-read sequencing data. It succeeds the Sequel system, offering significant improvements in throughput, accuracy, and flexibility. While a newer iteration, the PacBio Revio, offers even higher output for a lower price, the Sequel II remains a powerful option for various long-read sequencing needs.

Key Innovations

PacBio's Sequel II has key innovations that enhance both data generation and quality:

  • Improved chemistry: The Sequel II utilizes an enhanced Sequel II Chemistry 2.0 which enables higher yields of >Q30 HiFi reads per SMRT cell, longer read lengths of 15-20 kb, and increased detection of long isoforms for transcriptome sequencing projects.
  • Zero-mode waveguides (ZMWs): These microwells confine single DNA molecules for sequencing. The Sequel II uses redesigned ZMWs, offering better well utilization and higher data density, resulting in increased throughput per run.
  • Sequencing modes: The platform offers two sequencing modes: Continuous Long Read (CLR) sequencing for highly accurate, long reads with an emphasis on obtaining the longest reads possible and Circular Consensus Sequencing (CCS) for even greater accuracy through multiple passes of the same molecule.

Features and Technologies

The Sequel II boasts several improvements over its predecessor:

  • Higher throughput: Compared to the Sequel I, the Sequel II delivers higher max output.
  • Improved accuracy: The Sequel II offers base call accuracy exceeding 99% for high-quality bases in CLR mode, making it ideal for applications demanding high fidelity.
  • Flexible library prep options: The Sequel II is compatible with various PacBio library prep kits catering to diverse applications like whole-genome sequencing (WGS), transcriptome sequencing (RNA-seq), and targeted resequencing.

Intended Uses and Specific Applications

The Sequel II's long-read capabilities make it suitable for a wide range of NGS applications, including:

  • Whole-genome sequencing (WGS): De novo assembly, variant discovery, and structural variant analysis benefit from long reads that span repetitive regions often missed by short-read technologies.
  • Transcriptome sequencing (RNA-seq): Full-length transcript isoforms, alternative splicing detection, and complex gene fusions can be accurately characterized with long reads.
  • Targeted Sequencing: Long reads improve variant detection in complex regions like GC-rich areas or repetitive elements.
  • Epigenetics: Dedicated HiFi reads for methylation detection.

Compatible PacBio library prep kits include the SMRTBell Library HiFi prep and HiFi plex prep kits.

Comparison with Competing Instruments

Here's a brief comparison of the Sequel II with competing platforms offering similar read lengths:

  • PacBio Revio: The Revio offers much higher output at similar run times and accuracy. However, it tends to need a higher amount of input material per SMRT cell than the Sequel II.
  • Oxford Nanopore MinION: The MinION is a portable platform known for its long read capabilities. Although it can offer higher max output, it typically offers lower accuracy compared to the PacBio Sequel II. The MinION might be preferable for field-based research or real-time sequencing applications where portability is paramount, but accuracy is less critical.

Special Considerations

Researchers should consider the Sequel II if:

  • High-fidelity, long read data is paramount for their application.
  • Accuracy is more important than output, and the cost of the PacBio Revio outweighs the increased output that could be gained.
  • Portability is not a major concern, and the instrument's larger footprint is acceptable.

Need sequencing done on a PacBio Sequel II 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 29, 2024 and based on the spec sheets published by the manufacturer.