PacBio Sequel

Sequel is a sequencer released by Pacific Biosciences in January 2015. It is based on Single Molecule Real Time (SMRT) Sequencing.

PacBio Sequel
Photo of Sequel: by Pacific Biosciences


Manufacturer Pacific Biosciences
Technology Single Molecule Real Time (SMRT) Sequencing
Release date January 2015
Price [2] $350,000
MSRP as of release date
Type Industrial
Weight 354 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format BAM
Read length PacBio Sequel: 1x20000bp
Run time PacBio Sequel: Up to 20 hours
Reagent cost per Gb [1] PacBio Sequel: Unavailable
Data quality [3] PacBio Sequel: Up to 500,000 HiFi reads >99%* accuracy
Maximum output per run (Gb)[4] PacBio Sequel: 20.00
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

The PacBio Sequel system occupies a niche within the next-generation sequencing (NGS) market catering specifically to researchers requiring long-read sequencing. Unlike many NGS platforms that generate millions of short reads (often less than 300 base pairs), the Sequel leverages Single-Molecule Real-Time (SMRT) sequencing technology to produce significantly longer reads, averaging over 10,000 base pairs. This extended read length makes the Sequel ideal for applications where resolving complex regions of the genome or complete transcripts is crucial.

Key Innovations

The Sequel's core innovation lies in its zero-mode waveguides (ZMWs), part of SMRT technology. These microscopic wells confine single DNA molecules immobilized with fluorescently labelled DNA polymerase complexes. During sequencing, a laser illuminates the ZMW, exciting the fluorophore. As the polymerase incorporates nucleotides during DNA synthesis, the fluorophore releases a specific signal detected in real-time. This allows the sequencer to directly read the incorporation events, translating them into long stretches of DNA sequence data.

The Sequel represents a significant leap forward over its predecessor, the RS II, especially with respect to the increased ZMWs. The Sequel uses redesigned SMRT Cells to contain more than one million ZMWs, which is a significant increase over the 150,000 ZMWs within the RS II SMRT cells. This results in 6-7x as many reads per run on the Sequel.

Features and Technologies

The Sequel boasts impressive data quality metrics. PacBio's HiFi sequencing technology claims base accuracies exceeding 99.9%, making it suitable for variant detection and de novo genome assembly. Furthermore, the Sequel can process up to 16 SMRT cells per run.

Intended Uses and Specific Applications

The Sequel's long-read capabilities empower a variety of research applications, including:

  • De novo genome assembly: Reconstruction of complete genomes from scratch, particularly for complex genomes with repetitive regions.
  • Variant discovery: Identifying single nucleotide polymorphisms (SNPs) and structural variations, including large insertions, deletions, and inversions.
  • Transcriptome analysis: Characterization of full-length transcripts, including alternative splicing isoforms.
  • Metagenomics: Assembling genomes from complex microbial communities.

PacBio offers a variety of library preparation kits, such as the SMRTbell library prep for HiFi sequencing kits, tailored to these applications, ensuring optimized workflows for different sample types.

Comparison with Competing Instruments

  • PacBio Sequel II: The Sequel II is the direct successor to the original Sequel, offering significant improvements in data quality and throughput. It boasts higher read accuracy (>Q40) and increased data output per SMRT cell. However, the Sequel II comes at a slightly higher upfront instrument cost.
  • Oxford Nanopore MinION: The MinION is another long-read sequencer popular for its portability, compact size, low upfront cost and low running costs. It has a higher max output than the Sequel, but MinION reads are generally less accurate compared to the Sequel. Researchers requiring the highest accuracy and longest read lengths should prioritize the Sequel.

Special Considerations

Researchers would choose the PacBio Sequel over other sequencing platforms for the following reasons:

  • Need for long read lengths: The Sequel excels at generating reads exceeding 10,000 base pairs, crucial for applications like de novo genome assembly, full-length transcript analysis, and resolving complex structural variations.
  • High accuracy requirements: PacBio's HiFi sequencing technology delivers base call accuracies exceeding 99.9%, essential for variant discovery and confident gene annotation.
  • Studies involving complex genomes: The Sequel's ability to handle repetitive regions makes it ideal for assembling genomes with high GC content or those containing transposable elements.

Need sequencing done on a PacBio Sequel 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 26, 2024 and based on the spec sheets published by the manufacturer.