Chris Saunders

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

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

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.

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.

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...

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...

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:
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In Stockholm for work and got a great recommendation to Klättercentret Telefonplan for a boulder break last night. Great gym all around and easy hop on the metro from city center.

Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...

Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....

Very excited to share I’ll be starting my own group at University of Utah in the Department of Human Genetics in the new year! Reach out if you are interested! vollgerlab.com

Great keynote talk at #SFAF by Rob Knight, summarizing key innovations in microbiome research over the past decade.

One recent highlight is how long reads have transformed metagenome assembly, particularly #PacBio HiFi reads. The future is complete MAGs!

In addition to CNV recall and breakpoint accuracy improvements, this update boosts precision for large, unbalanced SVs and simplifies analysis by harmonizing all depth and breakpoint evidence into one consistent call set. The full update is now available in the most recent sawfish2 release on github

Just released a major update to the sawfish SV caller, which adds CNV calling and integration. Assessment on a set of pathogenic CNVs from Gross et al. shows this integrated-call strategy can substantially improve (single-method) recall, especially at lower HiFi sequencing depths

Human de novo mutation rates from a four-generation pedigree reference - Nature Analysis of more than 95% of each diploid human genome of a four-generation, twenty-eight-member family using five complementary short-read and long-read sequencing technologies provides a truth set t...

Long-read sequencing of large pedigrees is an ideal way to map all classes of denovo mutations! A collaboration between University of Utah, University of Washington, and PacBio. Glad to be a part of this project 👏

www.nature.com/articles/s41...

This example is hard to understand from e.g. IGV/Ribbon (see Fig1) but pretty simple in SVTopo: 4 blocks deleted (B,D,F,H), 2 inverted (E,G), 1 re-ordered (C)

Complex structural variant visualization with SVTopo Structural variants are genomic variants that impact at least 50 nucleotides and can play major roles in diversity and human health. Many structural variants are complex multi-breakpoint rearrangement...

I just released a new preprint! The manuscript describes SVTopo, a software tool that enhances visualization of complex SVs using HiFi data: www.biorxiv.org/content/10.1.... Here’s a summary of the results:

Last day to submit abstracts to #HiTSeq25 @hitseq.bsky.social #ISMB2025 - send us your work for an opportunity to present in the podium or poster.

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/PacificBiosc...

Hello bluesky world! Newbee here! I have a postdoc position immediately available in my lab. It will focus on identifying high-quality transposons in many genomes and finding their impacts in evolution and traits. Most works, including EDTA2 development and annotation of 400+ genomes, are done! 1/n

GitHub - ACEnglish/truvari: Structural variant toolkit for VCFs Structural variant toolkit for VCFs. Contribute to ACEnglish/truvari development by creating an account on GitHub.

🚀 Truvari v5.0 is here! 🎉
What’s new?
🔹 Enhanced symbolic variant support for <DEL>, <DUP>, <INV>
🔹 Robust BND comparison for cross-representation SV matching
🔹 Improved SV sequence similarity & HUGE SV support
🔹 Cleaner UI & Revamped API

👉 More: github.com/ACEnglish/tr...
#Genomics #Bioinformatics

Finally, a huge thank-you to all sawfish co-authors and the broader @pacbio.bsky.social team, our anonymous reviewers, SV community members, and users for their contributions, feedback and many helpful suggestions!

ESHG Conference 2025 ESHG 2022 COVID-19 Information Discover the ESHG 2025 - Hybrid Conference programme. We are proud to announce the confirmed 2025 speakers. Stay updated on matters related to the ESHG soc...

Also worth noting that a substantial new sawfish CNV integration feature will be coming as a preview release on GitHub later this month, which I’ll also be detailing as a poster presentation at ESHG. Looking forward to sharing more about this soon.

GitHub - PacificBiosciences/sawfish: Structural variant discovery and genotyping from mapped PacBio HiFi data Structural variant discovery and genotyping from mapped PacBio HiFi data - PacificBiosciences/sawfish

Since the preprint version of sawfish itself, we’ve released the full source code and now output all assembled contig alignments underlying the SV calls, in addition to several other stability and usability improvements. Sawfish binaries, documentation and source can be found on GItHub:

Since the preprint we’ve added several analyses including comparison to SV calling from global assembly, direct assessment of SV haplotype quality and SV context analysis, among others. To improve clarity, all SV calling and assessment results are now provided on Zenodo:

We also demonstrate how the sawfish quality model can be used to select for a high-quality 'sawfish HQ' call set, with an even higher proportion of concordant SVs (88%), while still retaining over 28000 pedigree-concordant SVs.

To assess multi-sample calling, we examined genotype pedigree concordance across SV calls from the 2nd and 3rd generations of CEPH-1463, finding that sawfish has over 9000 more pedigree-concordant calls compared to other methods while retaining the highest proportion of concordant SVs:

We assessed sawfish on the recent draft GIAB SV benchmark from the T2T-HG002-Q100 assembly, finding that it has the highest F1-score among evaluated callers on every tested SV size range and depth level. Other callers required at least 30x depth to reach sawfish’s accuracy at 15x:

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling AbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu

Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n)

doi.org/10.1093/bioi...

Very excited to see this study out in the world. We made what is (we think?) the first fully-humanized mouse model of a repeat expansion disorder, DRPLA, by replacing an entire copy of muring Atn1 with human ATN1 with 112 pure CAG repeats...
www.biorxiv.org/content/10.1...

Xiao Chen #ACMGMtg25 describing Kivvi tool for assembling long repeat units in medically relevant genes (KIV2 and D4Z4) using #PacBio HiFi reads. Large repeats accurately assembled!

‘Eloquent’ mice point to protein that may have shaped human speech Mice modified to have “human” version of a protein made more complex squeaks

My very first post on Bluesky Happy to be here. Check out our collaborative study with Bob Darnell @darnelr.bsky.social, where mice humanized for a NOVA1 gene variant unique to humans, produce more varied and complex vocalizations: www.science.org/content/arti...

www.nature.com/articles/s41...