Build your workflow with PacBio Compatible

PacBio is partnering with 10x Genomics through the 10x Compatible Partner Program and PacBio Compatible to unlock a multidimensional approach to sequencing at exceptional resolution and accuracy. This partnership demonstrates compatibility of the MAS-Seq for 10x Single Cell 3′ kit and Kinnex single-cell RNA kit for 10x Chromium singlecell libraries to be paired with PacBio’s long read sequencing platforms. The PacBio Onso sequencing platform is compatible with the 10x 3’ single cell RNA-Seq assay.

Agilent is a compatible partner for end-to-end targeted sequencing workflows including automation, library prep, and data analysis. This partnership leverages the ClearSeq Comprehensive Cancer panel and the accuracy of SBB technology to confidently identify disease-associated variants and optimize the molecular profiling of cancers. Targeted sequencing is enabled by Agilent’s SureSelect Custom DNA Target Enrichment Probes and PacBio’s sequencing by binding (SBB) technology. Additionally, Agilent’s Femto Pulse instrument is recommended for accurate generation of large-insert libraries for de novo large genome sequencing projects and other PacBio applications leveraging multi-kilobase read lengths.

SMRTbell Prep Kit 3.0 is automated on the Biomek i7 instrument.

BugSeq is a fully automated bioinformatics platform for microbiology labs. BugSeq powers the analysis of genomic and metagenomic data at global institutions with leading accuracy, cloud acceleration and intuitive analysis. The BugSeq platform is optimized for addressing the challenges of security, scalability, and collaboration in organizations that are pursuing genomic-based approaches to identify and characterize microbes. The BugSeq team is made up of experts in microbiology, computational biology and cloud computing who work tightly with partners to tackle some of the most exciting opportunities in microbiology, making it easier — and in many cases possible — to translate sequencing data into actionable results.

DNA Genotek Inc. provides biological sample collection devices for easy collection and stabilization of various sample types. High molecular weight DNA from saliva samples can be efficiently collected in the Oragene devices for extraction using the Nanobind kit. The extracted DNA is suitable for HiFi sequencing which requires high yield, quality, and purity DNA. Oragene devices are compatible with saliva extraction using the Nanobind PanDNA or CBB kits.

DNAnexus is a software partner with a platform to analyze large amounts of raw genetic data, share, collaborate, and integrate genetic data with other types of data, such as data from electronic medical records or imaging data. Analysis pipelines for PacBio data offered on DNAnexus include the PacBio WGS Variant Pipeline, TRGT, Paraphase, and Sentieon.

DNAstack is a software company that develops Omics AI, a modular software suite for integrating, sharing, and analyzing omics and health data. Omics AI is compliant with open standards developed by the Global Alliance for Genomics & Health. Workbench is a product within Omics AI that enables you to run best practices and custom analysis pipelines on data from PacBio and other instruments, in your own environment in Microsoft Azure, Amazon Web Services, Google Cloud, and on-premise.

Form Bio is a cutting-edge computational life sciences platform for research teams and enterprises. With an accessible, comprehensive, and collaborative platform alongside powerful AI-based solutions and bioinformatics services, Form Bio empowers scientists to efficiently and effectively harness the proliferation of data and computing power that has transformed the science of discovery. Analysis pipelines for PacBio data offered on Form Bio include the PacBio WGS Variant Pipeline and AAV QC.

Geneyx is a leading tertiary analysis platform tailored for high-fidelity long-read sequencing data. With a swift, high-throughput workflow, Geneyx analysis stands out for its ability to uncover insights from challenging unexplained cases through advanced processing, visualization, and analysis techniques coupled with updated annotations, phasing, and methylation analysis. Geneyx combines smart filtering and a novel phenotypic prioritization algorithm that integrates literature and machine learning to present the best candidate variant. Geneyx Analysis seamlessly integrates into any bioinformatic pipeline, making it a confident choice for HiFi data.

Golden Helix has been delivering industry-leading bioinformatics solutions for over a quarter century with thousands of users worldwide. Their software, VarSeq, enables the import and analysis of PacBio HiFi long-read sequencing. This capability facilitates a complete NGS testing suite for research samples with an increased precision and accuracy for variant calling, improved calling of structural variants and CNVs, and higher genomic definition with phasing and short tandem repeat calls.

Google Health is a strategic development partner for DeepConsensus integration into the PacBio Revio system. Google Health’s DeepVariant software analysis of PacBio HiFi data won best performance in variant calling for all benchmark regions in the Precision FDA Truth Challenge v2.

Hamilton workstations are compatible automation solutions for PacBio sequencing platforms. Hamilton and PacBio have partnered to develop walk-away automation solutions for both High Molecular Weight (HMW) DNA extraction on the Nimbus Presto and the SMRTbell Prep Kit 3.0 PacBio Library Preparation kits on the NGS Star to enable genomic workflows globally.

Shearing with the Megaruptor system leads to optimal long-read sequencing using PacBio systems prior to library preparation with the SMRTbell prep kits. The Megaruptor 3 system, recommended by PacBio for HiFi, microbial multiplexing and structural variants provides optimal DNA fragmentation from 5kb-100kb. The Megaruptor 3 comes with a default cassette that processes up to 8 samples at once, and Hologic Diagenode now offers a 12-sample cassette for 50% higher throughput that easily fits into your existing Megaruptor 3. The user-friendly system allows samples to be processed simultaneously without additional user input.

IDT has evolved as a leading DNA synthesis company to provide genomics solutions across NGS, CRISPR, Synthetic Biology, and PCR, equipping researchers with the right tools when they need them. Combining xGen high-conversion NGS library prep technology and the short-read PacBio Onso platform has demonstrated an ability to detect low allelic frequency variants in low input samples. IDT’s xGen targeted sequencing solution can also be combined with the PacBio Kinnex protocol for bulk RNA sequencing.

The MIRO CANVAS system is a compatible automation solution which uses digital microfluidics to provide walkaway library preparation for PacBio sequencing platforms. It fully automates PCR-free WGS library preparation of long DNA Fragments using PacBio’s SMRTbell Prep Kit 3.0 with 1-5 μg high quality, high molecular weight input DNA. The MIRO CANVAS system generates high quality results with total library quantity, HiFi yield, read length, read quality and structural variant detection comparable to manually prepared libraries.

The MP Biomedicals FastPrep 96 instrument offers a sophisticated high-throughput sample preparation solution tailored for PacBio long-read sequencing platforms. This instrument can shear up to 192 DNA samples at once, producing uniform, high-quality fragments, customizable to the desired size in as little as 8 minutes without requiring any supplementary reagents. Streamlining and simplifying the sample preparation process, the FastPrep 96 is compatible with the PacBio WGS workflow to deliver exceptional results.

NVIDIA’S invention of the GPU in 1999 sparked the growth of the PC gaming market, redefined modern computer graphics, and revolutionized parallel computing. More recently, GPU deep learning ignited modern AI — the next era of computing — with the GPU acting as the brain of computers, robots, and self-driving cars that can perceive and understand the world. NVIDIA is a data computation and storage partner of PacBio that has shown successful deep learning models to polish HiFi reads. PacBio sequencing data outputs can be analyzed by NVIDIA Parabricks, the only GPU-accelerated computational genomics toolkit for secondary analysis, which delivers fast and accurate analysis for sequencing centers, clinical teams, and researchers.

Opentrons robots are compatible with PacBio library preparation protocols. Opentrons and PacBio are partnering to automate the library prep for whole genome sequencing and Kinnex RNA sequencing on the Opentrons Flex NGS Workstation.

Parse Biosciences is a global life sciences company whose mission is to accelerate progress in human health and scientific research. Empowering researchers to perform single cell sequencing with unprecedented scale and ease, our pioneering approach is enabling groundbreaking discoveries in cancer treatment, tissue repair, stem cell therapy, kidney and liver disease, brain development, and the immune system. The growing portfolio of products includes Evercode Whole Transcriptome, Evercode TCR, Gene Capture, and a software tool for data analysis. Parse Evercode WT kits are compatible with PacBio Kinnex single-cell RNA library prep kits.

Qiagen is a partner for PacBio SBB workflows, providing end-to-end targeted sequencing including automation, library prep, and data analysis. Qiagen and PacBio are partnering on cfDNA workflows for the Onso sequencing platform.

Revvity offers vendor qualified, NGS library prep automated solutions for the PacBio HiFi Express Template Kit 2.0 and the SMRTbell Prep Kit 3.0.  Available from bench-top to fully automated sized-systems and designed for 8 to 384 sample throughput workflows, no programming or method development is needed by the user.  Revvity has hundreds of NGS workstations in the field and has a global team of NGS application, service, and sales experts.  With an ever-growing library of vendor qualified NGS library prep methods, Revvity is an ideal partner for NGS automation solutions.

Sage Science’s electrophoretic DNA size selection instruments provide user-adjustable DNA size distributions with outstanding rejection of small fragments. Optimally sized SMRTbell® libraries improve HiFi sequencing results, providing better uniformity and higher quality. PacBio recommends three systems for size selection. The BluePippin processes 4 samples with sample inputs up to 5 ug. For higher throughput needs, the PippinHT can process up to 22 samples in a single run. The SageELF (1 or 2 samples per run) fractionates an entire sample into 12 contiguous size bins, provides the most flexibility in sizing, and produces the narrowest size distributions.

Sentieon is a data analysis partner for processing and accelerating PacBio FASTQ to VCF data processing. Sentieon’s DNAscope tool takes advantage of the improved quality and long read length of PacBio HiFi reads to perform quick and accurate variant calling using specially calibrated machine learning models.

seqWell creates scalable genomics technologies that simplify workflows and help scientists to unlock transformative discoveries with sequencing. seqWell technology is focused on a novel, next-generation transposase, TnX, to drive the high-performance needs of tagmentation and advance NGS. seqWell offers a range of library prep products and fragmentation workflows that allow customers to quickly and easily scale their short- and long-read sequencing initiatives.

SMRTbell Prep Kit 3.0 is automated on the SPT Labtech firefly instrument. firefly is SPT Labtech’s all-in-one liquid handling platform for NGS library preparation that combines technologies for pipetting, dispensing, shaking and incubation into a single compact benchtop design. firefly sets a new standard in liquid handling software, featuring a visual, intuitive interface, and cloud-based protocol development and sharing.

Tecan offers multiplexed library preparation that is a compatible automation solution for PacBio sequencing platforms. The Tecan DreamPrep NGS Compact is a walkaway automation solution for NGS library prep with flexible configurations to deliver consistent, sequencing-ready libraries for a wide range of NGS protocols with minimal manual intervention that match different throughput requirements for your PacBio sequencer.

Thermo Scientific KingFisher purification instruments automate the extraction of DNA, RNA, proteins, and cells.  KingFisher instruments provide easy-to-follow protocols that remove manual steps and reduce overall processing time and errors associated with sample preparation while increasing the yield reproducibility of your results compared to the manual workflows.  KingFisher instruments are compatible with PacBio Nanobind HT kits.

PacBio has partnered with Twist Bioscience to deliver long-read target enrichment panels. The initial portfolio of products focuses on challenging, medically relevant genes (Dark Genes panel) and pharmacogenomics (Long Read PGx panel). Custom panel capability broadens access to the benefits of long-read HiFi sequencing like accurate variant detection including structural variants and phasing. This partnership also combines the outstanding accuracy of SBB technology with the Twist Exome 2.0 panel: 50x coverage of >80% target bases. By partnering with Twist, PacBio can deliver a targeted sequencing solution that is high throughput and cost-effective while also being supported end-to-end.

The varvis software is an IVDR Class C certified cloud-based platform for secondary & tertiary analysis of short- and long-read data. With proven analytical performance, it supports the automated raw data processing and variant calling of SNVs, CNVs, STRs, and SVs for HiFi data across diverse panel sizes, including WGS. Use virtual panels, customizable filtering buttons and inheritance patterns together with an AI based phenotypic prioritization to rank the detected variants. Leverage accurate phasing, STR counts and detailed variant annotations to accelerate your process. Additionally, the varvis software provides IVDR-compliant performance testing, automated quality control, training, and expert support.

Volta Labs is a genomics applications company partnering with PacBio to offer walk-away automation for PacBio library prep, enabling labs to scale sample prep for sequencing. Through preloaded apps on the Callisto Sample Prep System, a push-button sample prep solution for all NGS sequencing needs, PacBio customers are able to prepare high-quality PacBio libraries with less than 30 minutes of hands-on time and 5.5 hours of walk-away time. Users can be trained in minutes to generate PacBio libraries with minimal inter-operator variability.

Watchmaker Genomics applies advanced enzymology to enable breakthrough applications for the reading, writing, and editing of DNA and RNA. The product portfolio includes enzymes and kits for NGS library preparation, featuring solutions that are rapid, sensitive, and highly automatable. The Watchmaker DNA library prep portfolio is compatible with Onso sequencing to deliver superior sequence coverage and accuracy with a wide range of samples, including cfDNA and FFPE samples.

The LightBench, powered by Ranger Technology, is a three-in-one instrument offering automated DNA size selection, fragment length analysis and fluorometric quantification. It isolates size ranges of target DNA with industry-leading recovery and precision. LightBench excludes smaller fragments, optimizing long read inputs to deliver increased mean HiFi read lengths and data yields for PacBio sequencing platforms. To support an automated PacBio library prep workflow, the LightBench can be integrated into 3rd party liquid handling systems thanks to its SiLA 2-compliant API.