After 6 years, my time with PacBio came to an end last week. I'm proud of what I achieved - especially building the long-read #metagenomics program from scratch, and launching 5mC and 5hmC. However, all the positive interactions with the scientific community is what made this job truly meaningful.

A Scalable Framework for Species-Resolved Human Gut Microbiome Profiling Using Full-Length 16S rRNA Sequencing https://www.biorxiv.org/content/10.64898/2026.06.21.732309v1

Sharing results from a beta test of PacBio’s SPRQ-Nx reusable SMRT cells using two acquisitions! This increased SMRT cell throughput reduces sequencing costs for large human WGS projects. #ESHG2026 #PacBio #ESHG

Now live! Submit a 100 word proposal to win free #PacBio HiFi sequencing for #metagenomics. Long-read metagenomics is rapidly gaining traction and this is a great time to apply it to your research. programs.pacb.com/l/1652/2026-...

SPRQ-Nx chemistry is now shipping worldwide, bringing sub-$300 HiFi genomes to the Revio platform! This global rollout cuts sequencing costs by 30%, making it easier than ever to scale high-throughput workflows Full press release here: bit.ly/49HwmcL #SPRQNx #PacBio #HiFisequencing #Revio

Congratulations @wshuai.bsky.social and co-authors! We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint: www.biorxiv.org/content/10.6...

methbiome: reference-based DNA methylation profiling of long-read metagenomic data https://www.biorxiv.org/content/10.64898/2026.03.28.714822v1

PacBio is proud to partner with Basecamp Research to generate high-fidelity metagenomic data for the Trillion Gene Atlas, a landmark initiative to model biological data at the trillion-gene scale and accelerate AI-designed therapeutics. Learn more here: bit.ly/479RQh3 #PacBio #TrillionGeneAtlas

We’re launching the Trillion Gene Atlas with Anthropic, NVIDIA, PacBio, and UltimaGenomics. 🌍 The Goal: To expand known genomes 100×, sequencing 100M+ species to build foundation models grounded in evolution itself. 🔗 Read more: www.prnewswire.com/news-release...

We've seen a big increase in the number of long-read #metagenomics publications, especially those using #PacBio HiFi data. Also very encouraging to all the new tools for long-read metagenome assembly & taxonomic profiling. Complete list of publications: github.com/PacificBiosc...

#AGBTGM26 flash poster - Nick Renshaw from Wellcome Sanger on automated libray prep for PacBio Plex prep 96 kit. Use for microbial. Pacbio outperformed Illumina and ONT on assembly

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology

PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.

nature.com

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... 🧬💻🧪 github.com/RasmussenLab...

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much 1/

🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and @titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ? doi.org/10.1093/narg...

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations

Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru

doi.org

Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6) 👉 Preprint www.biorxiv.org/content/10.1... 👉 Github github.com/rolandfaure/...

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching

We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...

biorxiv.org

Excited to share our LongTrack study out in @natmicrobiol.nature.com today! Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/ 📄 rdcu.be/eL8mR

Long-read metagenomics for strain tracking after faecal microbiota transplant

Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...

rdcu.be

Another #metagenome assembly algorithm for #PacBio HiFi data - introducing Alice! I'll be very interested to see how this performs on some of our trickier datasets. More broadly, I'm happy to see continual development of tools for long-read #metagenomics. doi.org/10.1101/2025...

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching

We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an as-sembler that operates directly on these sketches. MSR produces...

doi.org

My new tool Paraviewer is now available for use at github.com/PacificBiosc...! If you use Paraphase, try this new next-step tool - it automates and greatly simplifies variant visualization from Paraphase variant calling. If you're at #ASHG2025, visit me today at poster 4109W. #pacbio

GitHub - PacificBiosciences/Paraviewer

Contribute to PacificBiosciences/Paraviewer development by creating an account on GitHub.

github.com

#PacBio announces major upcoming advances for #Revio and #Vega designed to lower genome costs, expand multiomic capabilities, and support regulated research. The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale. View the press release: bit.ly/4o06eyH

omicsomics.blogspot.com/2025/10/pacb... $300 LongRead personal genome via PacBio

#PACB PacBio Announces Major Advances for Revio and Vega to Lower Genome Cost and Expand Multiomic Capabilities https://www.stocktitan.net/news/PACB/pac-bio-announces-major-advances-for-revio-and-vega-to-lower-genome-ynph3qjnhmeq.html

PacBio Announces Major Advances for Revio and Vega to Lower Genome Cost and Expand Multiomic Capabilities

PacBio (NASDAQ: PACB), developer of the world's most advanced sequencing technologies, today announced innovations to its Revio and Vega

stocktitan.net

PacBio: $300 Genome Via Chemistry Update 🧬🖥️ omicsomics.blogspot.com/2025/10/pacb...

My complex variant visualization tool SVTopo is now officially published in BMC Genomics! link.springer.com/article/10.1.... This tool allows HiFi users to view complex germline structural variation in intuitive and informative plots.

Complex structural variant visualization with SVTopo - BMC Genomics

Background Structural variants are genomic variants that impact at least 50 nucleotides. Structural variants can play major roles in diversity and human health. Many structural variants are difficult to interpret and understand with existing visualization tools, especially when comprised of inverted sequences or multiple breakend pairs. Results We present SVTopo, a tool to visualize germline structural variants with supporting evidence from high-accuracy long reads in easily understood figures. We include examples of 101 visually complex structural variants from seven unrelated human genomes, manually assigned to ten categories. These demonstrate a broad spectrum of rearrangement and showcase the frequency of complex structural variants in human genomes. Conclusions SVTopo shows breakpoint evidence in ways that aid reasoning about the impact of multi-breakpoint rearrangements. The images created aid human reasoning about the result of structural variation on gene and regulatory regions.

link.springer.com

I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months! Aardvark: Sifting through differences in a mound of variants GitHub: github.com/PacificBiosc... Some highlights in this thread: 1/N

GitHub - PacificBiosciences/aardvark: A tool for sniffing out the differences in vari-Ants

A tool for sniffing out the differences in vari-Ants - PacificBiosciences/aardvark

github.com

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 10mo ago

Aardvark: Sifting through differences in a mound of variants https://www.biorxiv.org/content/10.1101/2025.10.03.680257v1

Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 10mo ago

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae https://www.biorxiv.org/content/10.1101/2025.09.30.679422v1

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut. Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals. doi.org/10.1101/2025...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

doi.org

Metagenomics for Microbiology 2nd Ed provides an opportunity to reflect on the growth of the metagenomics field, from new applications to technological advances. The chapters cover methodology, analysis, AI, omics, and more. shop.elsevier.com/books/metage... #microbiome #omics #DataScience

Metagenomics for Microbiology

Metagenomics for Microbiology, Second Edition unveils the intricate and diverse world of microbial communities, emphasizing their critical roles in he

shop.elsevier.com

Long and Kelsey just won the 2025 Microbiome SMRT Grant for HiFi shotgun metagenomics!! They will collaborate to optimize PacBio-compatible protocols for gut metagenomics, specifically generating high quality long-read data from IBD patients. Congrats to both! 🎉 🎉 www.pacb.com/blog/2025-mi...