By both improving accuracy and unifying assembly-based and mapping-based inferences, the portello approach has the potential to substantially improve analysis for rare-disease and other WGS applications. See our new preprint here:
doi.org/10.64898/202...
We also demonstrate the potential for improved CNV inference in a segmental duplication region where assembly-based read mapping substantially clarifies copy number inference compared to a conventional mapping approach. (4/5)
Small variant basepair errors comparison between conventionally mapped reads and portello-mapped reads.
We demonstrate that variant calling shows improved accuracy given these assembly-based read mappings. For instance, given the same set of input reads, DeepVariant calling from portello-mapped reads shows a 47% reduction in errors compared to calls from a conventional mapping process. (3/5)
Portello workflow schematic
Portello facilitates an assembly-based approach to read mapping, wherein reads mapped to their own diploid assembly contigs are transferred back to a reference genome. This approach allows standard secondary analysis tools and viewers to operate on reads mapped in the context of the diploid assembly
Comparison of read mappings at HG002 chr4:40,294,825-40,295,700, showing conventional (pbmm2) read mappings (above) and portello mappings (below). The same set of unaligned input reads were input into each mapping process.
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)
Dan Portik from #PacBio presents work on strand-specific 5hmC methylated base detection using PacBio HiFi sequencing, highlighting approaches for accurate epigenetic analysis with long reads.
See it today at #PAG33 β Poster P051, 3:00β4:30 PM.
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...
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 Ξ±-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
Nice to chat at CSHL last week. I missed the chance to tell you in person what a valuable resource these videos have been, I think I've seen every one. Even for well-known topics, the clarity of presentation can really sharpen intuition. Thanks for the great work.
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
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.
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:
1/N
In Stockholm for work and got a great recommendation to KlΓ€ttercentret 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 Iβll 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
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 π
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)
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.... Hereβs 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... π§¬π₯οΈπ§ͺ 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
π Truvari v5.0 is here! π
Whatβs new?
πΉ Enhanced symbolic variant support for <DEL>, <DUP>, <INV>
πΉ Robust BND comparison for cross-representation SV matching
πΉ Improved SV sequence similarity & HUGE SV support
πΉ Cleaner UI & Revamped API
π 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!
