PacBio RS

RS is a sequencer released by Pacific Biosciences in January 2011. It is based on Single Molecule Real Time (SMRT) Sequencing.

PacBio RS
Photo of RS: by PacBio


Manufacturer Pacific Biosciences
Technology Single Molecule Real Time (SMRT) Sequencing
Release date January 2011
Price [2] $695,000
MSRP as of release date
Type Industrial
Weight 1091 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format BAM
Read length PacBio RS: 1x10000bp
Run time PacBio RS: Up to 10 hours
Reagent cost per Gb [1] PacBio RS: Unavailable
Data quality [3] PacBio RS:
Maximum output per run (Gb)[4] PacBio RS: 0.10
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 RS

The Pacific Biosciences (PacBio) RS sequencer falls within the third-generation, or long-read, sub-segment of the next-generation sequencing (NGS) market. Launched in 2011, it was Pacific Biosciences first commercial product and has been surpassed by the subsequent RS II and Sequel II systems. While no longer actively supported by PacBio, the RS II can be a valuable tool for researchers requiring long reads for specific applications due to its continued availability and established protocols.

Key Innovation

The PacBio RS introduced a key innovation that propelled long-read sequencing forward:

  • Single Molecule Real-Time (SMRT) Sequencing: This core technology utilizes fluorescently labeled nucleotides that emit light upon incorporation into a growing DNA strand. The light pulses are detected in real-time, revealing the sequence without fragmenting the molecule. The strands don’t need to be fragmented, because there is an immobilized DNA polymerase/template complex inside thousands of wells called zero-mode waveguides (ZMW) that can measure the changes in light coming from the nucleotides as they’re incorporated.

Features and Technologies

The RS introduce several features to the sequencing scene:

  • Increased Read Length: The RS delivers average read lengths of ~2.5kb, although longer closer to 10 kb can certainly be achieved.
  • High Accuracy: PacBio was able to offer similar accuracy to short-read sequencing with the RS.

Intended Uses and Specific Applications

The RS caters to applications that benefit from long reads, including:

  • De novo genome assembly: Long reads enable reconstruction of complex genomes with fewer gaps and higher contiguity.
  • Transcriptome analysis: Full-length transcript isoforms and alternative splicing events can be unraveled with long reads.
  • Epigenetics: Long reads facilitate characterization of DNA methylation patterns across larger genomic regions.
  • Metagenomics: Unveiling complex microbial communities requires long reads to assemble complete genomes from diverse organisms.

For these applications, specific library preparation kits are available from PacBio, optimized for different sample types like DNA or RNA, and targeting specific research goals like whole-genome sequencing or targeted resequencing. Caution should be used, however, as PacBio is no longer officially supporting this instrument.

Comparison with Competing Instruments

Here's a quantified comparison of the RS with competing instruments:

  • PacBio Sequel II: Launched in 2020, the Sequel II boasts significantly higher data output per run (up to 10x), improved base calling accuracy, and higher read lengths on average compared to the RS II. However, the upfront instrument cost and reagent costs are also noticeably higher.
  • Oxford Nanopore Flongle: This portable sequencer offers even longer read lengths and higher max output but with lower accuracy and longer run times compared to the RS II.

Special Considerations

Although the RS can still be useful for researchers, especially when filling in gaps for genome assemblies, they should consider the following points when considering the RS:

  • Lower Throughput: Compared to newer instruments, the RS has a lower data output per run, impacting the time required to generate sufficient sequence data for large projects.
  • Discontinued Instrument: While the RS remains available from some vendors, it is no longer actively supported by PacBio. This means present reagents, future upgrades and technical support might be limited.

Need sequencing done on a PacBio RS 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.