Chris Saunders
@ctsa.bsky.social
Rare disease and cancer analysis models for sequencing data. Art school survivor. Views my own.
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
What if you could improve small variant accuracy, CNV inference, and interpretability of your HiFi WGS data by taking a different approach to read mapping? Our new preprint describes portello, a method which demonstrates the potential for such improvements. (1/5)
I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt: employment.utah.edu/salt-lake-ci...
Jobs | University of Utah
Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...
employment.utah.edu
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
Join us at this exciting Workshop on #LongReads with keynotes from @aphillippy.bsky.social @mydennis.bsky.social co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread #RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience
Long-Read Sequencing Workshop
The program will involve sessions on Genome Evolution, Genome Regulation, Transcriptomics, Rare Diseases, Common Diseases, and Viral and Microbial Genomes. Committed speakers include Adam Phillipy (NH...
jax.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
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
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
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 agoAardvark: Sifting through differences in a mound of variants https://www.biorxiv.org/content/10.1101/2025.10.03.680257v1
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....
Mumemto: efficient maximal matching across pangenomes - Genome Biology
Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the multiple...
genomebiology.biomedcentral.com
Vikram Shivakumar@vikramshivakumar.bsky.social · 2y agoExcited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.
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
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
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...
nature.com
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)
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...
biorxiv.org
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 · last yr.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
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
🚀 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
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
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...
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
doi.org
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!
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...
‘Eloquent’ mice point to protein that may have shaped human speech
Mice modified to have “human” version of a protein made more complex squeaks
science.org
Excited to announce our preprint describing SUPERB-SEQ 🦸, a new method to measure Cas9 edits and their effects on gene expression in single cells. Led by @micklorenzini.bsky.social and @bradbalderson.bsky.social www.biorxiv.org/content/10.1...
Joint single-cell profiling of CRISPR-Cas9 edits and transcriptomes reveals widespread off-target events and their effects on gene expression
A longstanding barrier in genome engineering with CRISPR-Cas9 has been the inability to measure Cas9 edit outcomes and their functional effects at single-cell resolution. Here we present Superb-seq , ...
biorxiv.org
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio. www.nature.com/articles/s41...
De novo designed proteins neutralize lethal snake venom toxins - Nature
Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...
nature.com
