2024 pacbio SMRT GRANT

MICROBIAL GENOMICS

The submission window is now closed!

Could your research benefit from highly accurate long-read sequencing at scale?

Apply to win free sequencing to advance your microbiome and metagenomics research.

Tell us in 100 words or less how PacBio HiFi sequencing for your project will advance your microbiome and metagenomics research, all for a chance to win sequencing for any of the following approaches:

SMRTbell library construction (up to 6 libraries) and HiFi sequencing (up to 3 Revio SMRT Cells) for metagenome-assembled genomes (MAGs) and Phase Genomics ProxiMeta Metagenome Deconvolution Platform (up to 6 libraries),
SMRTbell library construction (up to 96 libraries) and HiFi sequencing (up to 1 Revio SMRT Cells) for metagenome taxonomic and functional read-based profiling, or
Kinnex 16S rRNA SMRTbell library construction (up to 6 Kinnex 16S libraries, the number of 16S samples will be at the discretion of the Sponsors) and HiFi sequencing (up to 2 SMRT Cells 8M) for full-length 16S taxonomic profiling

PacBio offers complete end-to-end workflows at scale for any microbial genomics research, with the ability to sequence complete genomes and metagenomes with high accuracy.

Details on how to apply

We encourage scientists of any level to apply! Simply complete the short form on this page and include your 100-word proposal. You can read the official rules or reach out if you have any questions about this Microbial Genomics SMRT Grant. The submission window closes Monday, July 15, 2024 at 5:00 PM PDT.

The 2023 AAV STAR grant is open

Apply to win free sequencing and a travel stipend to enhance and promote your AAV-based gene therapy research

Tell us in 100 words or less how PacBio HiFi sequencing in your project will contribute to understanding and developing AAV-based gene therapies for a chance to be one of five winners of sequencing on one SMRT cell 8M and a travel stipend to present your work at a PacBio event.

PacBio offers a complete end-to-end workflow to characterize AAV preparations, with the ability to sequence full-length genomes with high accuracy.

Details on how to apply

We encourage junior academic scientists to apply! Simply complete the short form on this page and include your 100-word proposal. You can read the official rules, or reach out if you have questions about this STAR Grant. The submission window closes Wednesday, November 1, 2023 at 5:00 PM PDT.

Thank you to all participants!

In-person workshop

PacBio sequencing: See what you’ve been missing

Sunday, June 12, 2023 14:15–15:45 Room M 1+2, level 1

Speakers

PacBio sequencing and its applications

Neil Ward, GM and Vice President EMEA, PacBio

PacBio sequencing and its applications

Neil Ward, GM and Vice President EMEA, PacBio

PacBio sequencing and its applications

Neil Ward, GM and Vice President EMEA, PacBio

PacBio sequencing and its applications

Neil Ward, GM and Vice President EMEA, PacBio

PacBio sequencing and its applications

Neil Ward, GM and Vice President EMEA, PacBio

PacBio sequencing and its applications

Neil Ward, GM and Vice President EMEA, PacBio

PacBio sequencing and its applications

Neil Ward, GM and Vice President EMEA, PacBio

Plenary talks

Jacob Brandenburg, Senior Specialist, Segment Marketing, PacBio

Long-read whole genome sequencing (WGS) for plants and animals has allowed scientists to tackle the assembly of genomes ranging in size, ploidy, and repeat content. HiFi WGS enables complete, accurate, and contiguous assemblies of even the most complex genomes. As a result, HiFi WGS has been adopted by many biodiversity genomics consortia and agriculture researchers to assemble thousands of genomes.

While HiFi WGS simplifies the bioinformatics of genome assembly, library preparation remains a common challenge, especially for scientists sequencing organisms which yield low quantities of DNA or have very large genomes that require multiple libraries for a single de novo assembly.

We describe a new workgow using the PacBio SMRTbell prep kit 3.0 that is amenable to automation while significantly reducing the time (by 50%), cost, and DNA quantity (by 40%) necessary to prepare a sequencing library. We applied the workflow to rice and fly samples and demonstrate that the assembly quality matches that of the previous, more time-consuming library prep workgows. This new workflow offers a more efficient solution for all WGS applications, regardless of organism size or complexity.

Greg Concepcion, Staff Engineer, Bioinformatics, PacBio

With the increasing prevalence of high-quality assembled genomes, access to the pangenomes of species is now an achievable possibility for researchers with all research budgets. However, the tools to visualize, analyze, and extract actionable information from these pangenome datasets are still in their infancy. Using a large plant pangenome dataset, we evaluated the pangenome graph builder pipeline for building a pangenome graph of the species and use these evaluations to provide basic recommendations for how to best manipulate and visualize these pangenomic datasets with other downstream tools including the vg toolkit.

Greg Concepcion, Staff Engineer, Bioinformatics, PacBio

With the increasing prevalence of high-quality assembled genomes, access to the pangenomes of species is now an achievable possibility for researchers with all research budgets. However, the tools to visualize, analyze, and extract actionable information from these pangenome datasets are still in their infancy. Using a large plant pangenome dataset, we evaluated the pangenome graph builder pipeline for building a pangenome graph of the species and use these evaluations to provide basic recommendations for how to best manipulate and visualize these pangenomic datasets with other downstream tools including the vg toolkit.

Greg Concepcion, Staff Engineer, Bioinformatics, PacBio

With the increasing prevalence of high-quality assembled genomes, access to the pangenomes of species is now an achievable possibility for researchers with all research budgets. However, the tools to visualize, analyze, and extract actionable information from these pangenome datasets are still in their infancy. Using a large plant pangenome dataset, we evaluated the pangenome graph builder pipeline for building a pangenome graph of the species and use these evaluations to provide basic recommendations for how to best manipulate and visualize these pangenomic datasets with other downstream tools including the vg toolkit.

Presentations

Monday, June 12, 2022 14:15–15:45 PST

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Elizabeth Tseng, PhD

Title, credentials, PacBio

Elizabeth Tseng, PhD

Title, credentials, PacBio

Elizabeth Tseng, PhD

Title, credentials, PacBio

Elizabeth Tseng, PhD

Title, credentials, PacBio

Presentations + posters

Poster presentations

#	Title	First Author	Date/Time
2314	Increased Diagnostic Yield With Long Read Sequencing In Patients With Undiagnosed Neurodevelopmental Disorder	S. Jamuar	October 26, 3:00 - 4:45 pm PDT
2322	Long-read HiFi genome sequencing reveals a 2.7 kilobase intronic insertion in NR5A1as a cause of 46,XY disorder of sexual development	G. Del Gobbo	October 26, 3:00 - 4:45 pm PDT
2354	Ultra-low DNA input with long-read sequencing identified complex chromosomal rearrangements involving NIPBL in a Cornelia de Lange syndrome patient	N. Jiang	October 26, 3:00 - 4:45 pm PDT
2723	Accurate CYP2D6 star (*) allele diplotyping for long-read PacBio HiFi sequencing	J. Harting	October 26, 3:00 - 4:45 pm PDT
3096	PacBio HiFi sequencing provides highly accurate CpG methylation calls without bisulfite treatment	C. Saunders	October 26, 3:00 - 4:45 pm PDT
3133	Sequencing By Binding (SBB) enables a lower limit of detection for Tuberculosis resistance genes gyrA and katG	C. Wike	October 26, 3:00 - 4:45 pm PDT
2269	Clinical long-read genome sequencing: Analytical performance of germline small variant detection using HiFi genome sequencing	N. Hammond	October 27, 3:00 - 4:45 pm PDT
2954	De novo variant detection with HiFi reads	J. Lake	October 27, 3:00 - 4:45 pm PDT
3012	High throughput workflow for human whole genome sequencing using PacBio HiFi	J. Rocha	October 27, 3:00 - 4:45 pm PDT
3132	Sequencing By Binding (SBB) demonstrates superior performance in low-pass whole-human-sequencing applications	KY. Chen	October 27, 3:00 - 4:45 pm PDT
2938	Closing the gap: Solving complex medically relevant regions of the human genome	F. Sedlazeck	October 27, 3:00 - 4:45 pm PDT

In-booth presentations

#	Title	First Author	Date/Time
2314	Increased Diagnostic Yield With Long Read Sequencing In Patients With Undiagnosed Neurodevelopmental Disorder	S. Jamuar	October 26, 3:00 - 4:45 pm PDT
2322	Long-read HiFi genome sequencing reveals a 2.7 kilobase intronic insertion in NR5A1as a cause of 46,XY disorder of sexual development	G. Del Gobbo	October 26, 3:00 - 4:45 pm PDT
2354	Ultra-low DNA input with long-read sequencing identified complex chromosomal rearrangements involving NIPBL in a Cornelia de Lange syndrome patient	N. Jiang	October 26, 3:00 - 4:45 pm PDT
2723	Accurate CYP2D6 star (*) allele diplotyping for long-read PacBio HiFi sequencing	J. Harting	October 26, 3:00 - 4:45 pm PDT
3096	PacBio HiFi sequencing provides highly accurate CpG methylation calls without bisulfite treatment	C. Saunders	October 26, 3:00 - 4:45 pm PDT
3133	Sequencing By Binding (SBB) enables a lower limit of detection for Tuberculosis resistance genes gyrA and katG	C. Wike	October 26, 3:00 - 4:45 pm PDT
2269	Clinical long-read genome sequencing: Analytical performance of germline small variant detection using HiFi genome sequencing	N. Hammond	October 27, 3:00 - 4:45 pm PDT
2954	De novo variant detection with HiFi reads	J. Lake	October 27, 3:00 - 4:45 pm PDT
3012	High throughput workflow for human whole genome sequencing using PacBio HiFi	J. Rocha	October 27, 3:00 - 4:45 pm PDT
3132	Sequencing By Binding (SBB) demonstrates superior performance in low-pass whole-human-sequencing applications	KY. Chen	October 27, 3:00 - 4:45 pm PDT
2938	Closing the gap: Solving complex medically relevant regions of the human genome	F. Sedlazeck	October 27, 3:00 - 4:45 pm PDT

Visit us at booth X5-364

Stop by our booth to chat with PacBio staff and have your questions answered. We are excited to learn about your sequencing goals and learn more about your research.

Thank you to our co-sponsors: Colossal Biosciences, as well as The Vertebrate Genomes Laboratory out of The Rockefeller University for supporting the 2024 PacBio SMRT Conserve Grant.

Colossal is a breakthrough bioscience and genetic engineering company that creates disruptive technologies for extinct species restoration, critically endangered species protection, and the repopulation of critical ecosystems that support the continuation of life on Earth.

The Vertebrate Genomes Laboratory (VGL), directed by Dr. Olivier Fedrigo, serves as a central laboratory for the VGP. The G10K consortium, an international consortium of tissue curators, biologists, conservationists, genome scientists, computer scientists, outreach educators, and more leads the VGP. Dr. Erich Jarvis is the current chairperson of the G10K consortium. The G10K leadership and community of scientists built an infrastructure from sample collection to genome sequencing, assembly, annotation, alignments, public data releases, and analyses for publications. In addition to the VGL, the genome sequencing hubs also include the Sanger Institute in the UK and the Max Planck Institute in Dresden, Germany.

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