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

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

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

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

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

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:

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!

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 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!

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

Something that's been bugging me for a while in bioinformatics data analysis is this overreliance on packages, workflows and what's been called "cargo cult science". Can we have more conceptual thinking, more theory? Asking for what we really want to achieve and what we need to do gets us there.

HiFi long-read genomes for difficult-to-detect clinically relevant variants https://www.medrxiv.org/content/10.1101/2024.09.17.24313798v1

The preliminary #eshg25 program is online. Stellar line-up of invited speakers - full breadth of our amazing field. Grateful to a wonderful SPC @eshg that made this possible. See you all in Milan next year! 2025.eshg.org/programme-at...

I thought it could be nice to connect the community of researchers in human genetics, so here is the Genetics Starter Pack! 🧬 #academicsky Let me know if you would like to be added or know someone to add. Enjoy and share! go.bsky.app/LN2NRuB

Looking for a starter pack to find/join a community? Here is a searchable/browsable link. Love this feature of @bsky.app blueskydirectory.com/starter-pack...

Try this: move the BlueSky app icon to where your Twitter icon is. Then slide your Twitter icon off your main screen. You’ll notice a vast improvement in your blood pressure.

Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use! www.biorxiv.org/content/10.1...

Work by Nate Brown, @vikramshivakumar.bsky.social and I showing how compressed full-text indexes like the move structure can be extended to report "chaining" information alongside exact matches. The extension is called "col-BWT" (1/3)

If you were interested but missed it: www.pacb.com/wp-content/u...

#ASHG2024 was a blast. I had great discussions with friends and #pacbio collaborators, presented a poster on my new tool SVTopo, welcomed #PacBioVega to the world, and realized than I'm a bigger fan of One Republic than I knew before. Excited for next time!

Analyzing @pacbio.bsky.social Kinnex full-length (bulk) RNA-Seq data? Here's the troubleshooting guide to help you understand the metrics! Explanation on FLNC reads, SQANTI3/pigeon classification, and artifact filtering. #Bioinformatics 🧬🧪 www.pacb.com/wp-content/u...

A little birdie told us we should migrate to bluer skies. 😉 Hello Bluesky world. 👋🌎 Please re-share this post so we can follow you and help to grow the genomics community on here! 🧬✨

Please share broadly! We (Molecular Genetics, University of Toronto) are looking for a new faculty member! Deadline Dec 19. Those working on model organisms and using genomics, computational and systems approaches are strongly encouraged to apply! Reach out w/ Qs! jobs.utoronto.ca/job/Toronto-...

I created a long-read sequencing starter pack. I'm still finding people on here, so apologies if I missed you. Please suggest people who should be added and I'll add them! go.bsky.app/JGkefsJ

We just added a methylation segmentation algorithm for PacBio HiFi data to our MethBat tooling (beta). If you are interested in trying it out, we would greatly appreciate any feedback on the performance and possible extensions! Release here: github.com/PacificBiosc...

Very excited to see a new metagenome asssembly algorithm available for PacBio HiFi data! metaMDBG performs extremely well based on my benchmarks and we plan on using it for several deep-sequencing projects. doi.org/10.1038/s415...

A reminder of this faculty opening in the Dept of Human Genetics at UU. Applications are due Dec. 8. Please share!

Tandem repeats are hard! Get your benchmark from @genomeinabottle.bsky.social to compare caller : biorxiv.org/content/10.1... 1.7 mil TR catalog; new tooling to overcome variant representation issues (SNV &SV); insight in complexity. First time we can compare across different techs/caller!

I'm pleased to announce the release of HiPhase v1.0.0!  In addition to phasing small and structural variants from #PacBio #HiFi datasets, HiPhase now also includes support for phasing short tandem repeats (#STR) at the same time!   Full release notes can be found here: github.com/PacificBiosc...

Looking forward to seeing everyone at #ASHG23 next week! This will be my first time attending, and we have some exciting news to share about HiPhase for #PacBio HiFi datasets…

I am looking for a graduate student and a postdoc to join my group! We are a computational group working on understanding evolution in natural populations with a large emphasis on the microbiome. Please get in touch by dm or email! garud.eeb.ucla.edu