PacBio WGS

The PacBio WGS pipeline is the best option for large-scale, complex eukaryotic genomes such as amphibians, birds, reptiles, mammals, etc., and is also a great option for all organisms when aiming for reference-quality assemblies. We generally recommend a minimum target depth of 15-20x for data that can later be assembled into publication-quality genomes. 

Our PacBio WGS pipeline uses PacBio’s SMRTbell prep kit 3.0 for circularized library prep and relies on the Megaruptor 3 shearing technology with adjustable fragment length to produce HiFi reads via CCS. This library preparation and sequencing strategy is very sensitive to both DNA fragment size and sample contaminants. To produce high-quality samples compatible with this platform, we recommend careful consideration of extraction methods, fragment analysis before submission, and shipping on dry ice.  For more prep tips and expected fragmentation sizes, see the additional information below the services table. 

Uniform fragment size is a necessary part of producing HiFi reads for CCS. In order to balance this requirement with the goal of maximizing read lengths for each project, SeqCenter requires each project to be run on its own PacBio flowcell with multiplexing only libraries of the same sample type from the same customer. Each order will need to include one library preparation per sample and at least one flowcell, and every library preparation service is indexed to allow for multiplexing on any flowcell. 

Sample Requirements:

  • At least 1 µg total dsDNA
  • Maximum volume of 100 µL

What You Will Receive:

  • One fastq file for each sample
  • One bam file with run metric data
  • Sequencing stats summary
  • Materials and methods summary
  • Data shared via Box folder within 2 weeks

Packages & Pricing

Sequencing Package Price*
Sequel Ile 8M Flowcell
Run across a Full Flowcell. Library preparation separate.
Revio 25M Flowcell
Run across a Full Flowcell. Library preparation separate.
PacBio WGS Library Preparation
Includes QC and barcoding. One needed per sample. Sequencing separate.
*Orders >48 Samples receive 5% discount

To help our customers meet the strict sample requirements, SeqCenter offers convenient HMW DNA extractions using PacBio’s Nanobind Tissue kit, which is specifically meant for use with PacBio library preparation. While we have had success with this kit with many bacterial samples, this kit is not broadly applicable. However, other options are available for some sample types where special considerations need to be made. See the extraction section below for more details.

We are able to accommodate all organisms up to BSL2+ and do not accept BSL3 or higher classified organisms for extraction services. Samples requiring DNA extraction can be submitted as aspirated cell pellets shipped frozen on dry ice or as growth on sealed nutrient agar plates shipped at ambient temperature. A minimum of 109 cells is recommended for all microbial DNA isolation submissions. We cannot culture samples. We encourage you to ensure samples are pure and that there is adequate growth on your plates before shipping.

PacBio naturally lends itself to genomic assembly projects, especially for complex and repeat-rich regions. We routinely produce well-annotated genome assemblies for bacterial and fungal samples and are happy to discuss the options available for collapsed assemblies of higher-order eukaryotes.

Assemblies also offer the opportunity for 4mC and 6mA methylation site predictions, though this goal must be noted before sequencing for the necessary data to be captured.

For additional information on our bioinformatic capabilities with PacBio data, please see our Bioinformatics Services page.

Considerations for Successful WGS PacBio Sequencing

The PacBio platform has some of the most stringent sample requirements of all of the DNA sequencing platforms we host. The extraction method and clean-up often have the greatest influence on sample quality in terms of purity and fragment length.

Beyond intolerance for the standard contaminants that can interfere with enzymatic reactions (like phenolates), common problem constituents that are carried over during extraction include RNA and polysaccharides. For samples with high RNA content, a simple RNase treatment is recommended before submission.

Polysaccharide contamination is a more difficult problem to remedy. Carryover is common for fungi, plant, insect, and crustacean samples, though it is possible for any organism with polysaccharides embedded in its cells, tissues, or extracellular matrices. Clean-up post extraction is more difficult than during, so we recommend choosing an extraction method that addresses this, such as a CTAB method or PacBio Nanobind extraction kit with necessary protocol modifications. PacBio’s technical support can provide modified protocols specific to your sample type.

Long starting fragment lengths optimize total output and fully utilize all of the benefits of the PacBio platform and prep. To minimize initial fragmentation, we recommend choosing an HMW (high molecular weight) extraction option for your sample, as these are often the gentlest methods. We strongly encourage this approach over more brute-force methods like bead beating. For particularly difficult samples, HMW extractions may require special modifications and extra considerations. We also strongly encourage customers to analyze fragment length before sample submission to assess how additional unavoidable fragmentation will affect read length.

Expected Fragmentation by Sample Type

When ordering PacBio WGS, we strongly encourage you to include your sample type (e.g., metagenomic, cell culture, origin, etc.), organism, and extraction method. This information will help us fine-tune the fragmentation process to provide maximum read length and total output. Below are some examples of sample types, typical extraction methods we see, and average read length that might be expected.

Sample Type Typical Extraction Method Expected Read Length
Metagenomic Bead-beating, physical lysis 2-6 kbp
Bacterial cell culture Enzymatic, column-based, or HMW 6-10 kbp
Plant HMW kit, Nanobind Plant kit Up to 18kbp

PacBio and Amplicon Libraries

The PacBio SMRTbell prep 3.0 kit can support sequencing of amplicon libraries with modifications to our standard workflow to remove fragmentation. Due to skew for overrepresentation of smaller fragments and possible flowcell failure, it is strongly recommended that library lengths differ by no more than 10%.

To ensure proper processing of amplicon libraries, please note that the sample is an amplicon library and that fragmentation should not be performed. For additional information, please contact us.

PacBio Sequencing and Modified Bases

PacBio’s SMRT technology is capable of capturing raw methylation kinetics that can later be used to predict 4mC or 6mA base modifications. In order to store this data, the sample must be flagged for this option in advance of sequencing, so customers must indicate that the optional data should be stored for their samples when placing an order. Post-sequencing, predictions can be made in relation to an assembly but cannot be placed on individual reads. For additional information about SeqCenter’s add-on services for methylation calling, please see the PacBio Long Read portion of our Assembly and Annotation page.

Additional Resources

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