The worst AG so far...

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)

Please spread the word — a 2-year postdoctoral fellowship is available in my group funded by the Simons Foundation Autism Research Initiative (SFARI) to perform a study testing the contribution of functional non-coding variants in glutamatergic neurons to autism. 1/3

Complex genes can hide critical insights. Hear Xiao Chen from #PacBio explain how Paraphase with HiFi sequencing resolves paralogs and pseudogenes.

Don’t miss her #ASHG25 poster on D4Z4 repeat resolution in facioscapulohumeral muscular dystrophy!

Watch: bit.ly/4mHVhAe

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

he Department of Plant Pathology at the University of California, Davis is seeking applications for a fulltime, tenure-track Assistant Professor position in Mycology, with a focus on plant pathogenic, symbiotic, or mycotoxigenic fungi and fungal-like organisms (e.g., oomycetes). We are looking for a highly motivated and creative scientist with a strong background in mycology and/or the biology of fungi and fungal-like organisms that interact with plants. The successful candidate will be expected to develop a world-class, externally funded research program that integrates both fundamental and applied aspects of fungal biology within the context of plant pathology. We welcome applicants pursuing a wide range of research topics related to plant-associated fungi, including but not limited to mechanisms of fungal pathogenesis or symbiosis with plants, population genomics and evolution of fungal plant pathogens, plant-associated fungal microbiomes and plant-microbe interactions, and/or one health approaches to fungal diseases and antifungal resistance. Applicants working in other relevant research areas involving pathogenic, symbiotic, or mycotoxigenic fungi or fungal-like organisms that affect plant health are also encouraged to apply. The successful candidate will have significant opportunities for collaboration with faculty in plant pathology, microbiology, genomics, and agricultural sciences, and to contribute to addressing issues of importance to California’s agricultural and natural ecosystems. The appointee primary teaching responsibilities will be teaching Introductory Mycology, an upperdivision lab class, and SAS 30, Mushroom, Molds & Society, a general education class for non-majors. Additional graduate and undergraduate teaching responsibilities may be assigned based on departmental needs and the candidate’s expertise. The department offers modern instructional facilities, including a newly renovated teaching laboratory.

Please repost -- The Univ. California Davis dept of Plant Pathology is hiring a Fungal biologist / Mycologist

Applications due Dec 1

Application portal: recruit.ucdavis.edu/JPF07339

Screenshot shows part of the job posting (with alt-text of the same text)

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

Phishing site : minimap2.com · Issue #1316 · lh3/minimap2 Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...

minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...

The human #microbiome holds enormous potential, but only if we can see it clearly.

Join this webinar to learn how #PacBio HiFi sequencing delivers accurate, high-resolution insights with 16S rRNA sequencing and shotgun metagenomics.

Secure your spot: bit.ly/4mYmK1G

The Platinum Pedigree: a long-read benchmark for genetic variants. #HumanGenome #ReferenceGenome #PlatinumPedigree #LongReads #Benchmarking #GeneticVariants @natmethods.nature.com 🧬 🖥️
www.nature.com/articles/s41...

Buongiorno Milano! Ready for a great day 1 of #eshg2025?
Packed program of excellent science 8.30am-8.00pm - plus networking event till 9.30pm to meet many friends, colleagues and collaborators! …andiamo @eshg.bsky.social @eshgyoung.bsky.social

Dr Farrow uses @pacbio.bsky.social tools and pipelines in her clinically validated HiFi WGS tests. Shout out to @williamrowell.dev @egor-dolzhenko.bsky.social @guilhermesena1.bsky.social Xiao Chen @meberle.bsky.social

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 to understand the most fundamental processes underlying human genetic variation.

Nature research paper: Human de novo mutation rates from a four-generation pedigree reference

https://go.nature.com/3GnaA22

Our Nature paper (rdcu.be/ei1NM) deep sequencing a 4-generation, 28-member family using multiple sequencing technologies to study transmission of all classes of genetic variation is out! @uwgenome.bsky.social @hhmi.org @pacbio.bsky.social @utah.edu

4 generations help science explore genome mutation rate - UW Medicine | Newsroom

Advanced genomic analysis of 4 generation family offers new knowledge about genetic mutations & their transmission, including inherited variants & those that arise anew
@nature.com @uwgenome.bsky.social @eichlerlab.bsky.social @uwmedicine.bsky.social @utah.edu @pacbio.bsky.social

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:

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...

Few more days from now everyone - join us in Milan — submit an abstract by Monday!

HiFi long-read genomes for difficult-to-detect, clinically relevant variants Detecting pathogenic germline variants in the clinic remains technically challenging. We analyzed 145 previously identified, hard-to-detect variants in 100 samples using HiFi long-read sequencing (LRS...

Image a set of 100 rare disease cases with the most difficult-to-detect mutations a human genetics lab can be faced with. …many of which very difficult or even impossible to detect with (short-read) sequencing methods, and/or requiring additional orthogonal tests…

www.cell.com/ajhg/abstrac...

I’ll be at PAG 2025 presenting on #longread #microbiome species profiling with a talk and a poster. I’ll also be at the PacBio booth some and the party (link to register in reshared post below). Come see me if you or a colleague will be attending. programs.pacb.com/pag2025

Very excited (and a bit nervous) to announce that I will be hiring two Postdocs for my new group(!) in Copenhagen to study the Neanderthal and Denisovan DNA which survives in present-day humans. Retweet will be much appreciated :)

Link for application:
candidate.hr-manager.net/ApplicationI...

I've been informed the DOI link is not working yet, here's the bioRxiv URL in the interim:
www.biorxiv.org/content/10.1...

Great work by @holtjma.bsky.social to create this PGx caller, StarPhase. Special thanks to the many collaborators who shared data and provided feedback on how to improve the accuracy and user experience.

I'm very impressed by the thorough work @holtjma.bsky.social, @meberle.bsky.social and team have done in building #StarPhase - it really checks all the boxes for reliable calling of #pharmacogenomic star alleles, even for #CYP2D6! 🙌

Biology of Genomes Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

Biology of Genomes 2025 is coming up:
- meeting dates: May 6 - 10, 2025
- abstract deadline: Feb 14, 2025
We hope to see you there for another great meeting with a fantastic speaker lineup!

meetings.cshl.edu/meetings.asp...

Post-doc opportunity! 📣📣📣 Our host-virus interaction lab (Institut Cochin, France) is seeking a highly motivated post doctoral researcher for a 2-year position to work on HIV latency. Join us in exploring cutting-edge molecular mechanisms in the beautiful city of Paris!

Recruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics | Children’s Hospital of Philadelphia Recruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics in Philadelphia, Pennsylvania, United States. null at Children’s Hospital of Philadelphia

Late-stage graduate students and junior postdoctoral fellows are invited to attend the 2025 Recruitment Summit for CHOP/Penn Postdoctoral Scholars in Cell Biology and Genomics

careers.chop.edu/us/en/event/...

Application review starts 11/30! Please share, new Bluesky friends!

@sedlazeck.bsky.social AMPath24 talk about long reads highlighting TRGT tool by @egor-dolzhenko.bsky.social and @guilhermesena1.bsky.social and others for HiFi sequencing by @pacbio.bsky.social

Looking at that and realized that was B&O espresso and I lived right across the street.