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Reposted by Chris Saunders

Jon Belyeu @jonbelyeu.bsky.social · 7h

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

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Reposted by Chris Saunders

Dan Portik @dportik.bsky.social · 8d

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

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Reposted by Chris Saunders

Matt Holt @holtjma.bsky.social · 3d

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

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Chris Saunders @ctsa.bsky.social · 4d

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.

Reposted by Chris Saunders

Adam Phillippy @aphillippy.bsky.social · Jun 17

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...

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Reposted by Chris Saunders

Ben Langmead @benlangmead.bsky.social · Jun 17

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....

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Reposted by Chris Saunders

Mitchell R. Vollger @mrvollger.bsky.social · Jun 5

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

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Reposted by Chris Saunders

Dan Portik @dportik.bsky.social · May 22

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!

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Chris Saunders @ctsa.bsky.social · May 20

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

GitHub - PacificBiosciences/sawfish: Joint structural variant and copy number variant caller for HiFi sequencing data

Joint structural variant and copy number variant caller for HiFi sequencing data - PacificBiosciences/sawfish

github.com

Chris Saunders @ctsa.bsky.social · May 20

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

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Reposted by Chris Saunders

inversion.bsky.social @inversion.bsky.social · Apr 23

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...

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...

www.nature.com

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Reposted by Chris Saunders

Jon Belyeu @jonbelyeu.bsky.social · Apr 22

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)

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Reposted by Chris Saunders

Jon Belyeu @jonbelyeu.bsky.social · Apr 22

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:

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...

www.biorxiv.org

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Reposted by Chris Saunders

Francisco De La Vega @ribozyme.bsky.social · Apr 17

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.

Francisco De La Vega @ribozyme.bsky.social · Apr 12

Submit your abstract to HiTSeq at ISMB 2025 (July 20–24, Liverpool, UK)! Topics: short/long read analysis, assembly, variant detection, methylation, metagenomics, oncology, tools & more. Open to academia + industry. Deadline: April 17!
www.hitseq.org

HiTSeq 2025: Conference on High Throughput Sequencing Algorithms and Applications - Home

www.hitseq.org

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Reposted by Chris Saunders

Stephen Turner @stephenturner.us · Apr 11

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

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Reposted by Chris Saunders

Shujun Ou @sigmafacto.bsky.social · Apr 10

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

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Reposted by Chris Saunders

acenglish.bsky.social @acenglish.bsky.social · Jan 10

🚀 Truvari v5.0 is here! 🎉
What’s new?
🔹 Enhanced symbolic variant support for , ,
🔹 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

GitHub - ACEnglish/truvari: Structural variant toolkit for VCFs

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

github.com

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Chris Saunders @ctsa.bsky.social · Apr 10

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!

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Chris Saunders @ctsa.bsky.social · Apr 10

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.

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...

2025.eshg.org

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Chris Saunders @ctsa.bsky.social · Apr 10

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:

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

github.com

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Chris Saunders @ctsa.bsky.social · Apr 10

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:

Sawfish publication SV VCFs and assessment results

This tarball "sawfish_publication_sv_vcfs_and_assessments.tar.gz" contains structural variant VCFs from the sawfish manuscript analyses, as well as the corresponding VCF assessment results and assessm...

doi.org

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Chris Saunders @ctsa.bsky.social · Apr 10

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.

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Chris Saunders @ctsa.bsky.social · Apr 10

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:

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Chris Saunders @ctsa.bsky.social · Apr 10

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:

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