Mike Schatz

Population-scale Long-read Sequencing in the All of Us Research Program The All of Us Research Program (AoU) is a national biobank seeking to enroll one million individuals in the United States to link genomic and biomedical data, including short- and long-read whole-geno...

Read the preprint here with all the details, plus lots of other long-read powered analysis! www.medrxiv.org/content/10.1...

This uncovers strong links between population-enriched SVs and conditions such as metabolic disease, cardiovascular disorders, and immune phenotypes. Huge thanks to the whole team co-led by Kiran Garimella, @sedlazeck.bsky.social, Michael Talkowski, Evan Eichler, and me.

We call SVs from PacBio HiFi long read data, and then impute into 10k AoU short-read datasets with EHR data to identify 291 SV–disease associations across 226 traits, with over half absent from the short-read callset. Fine-mapping revealed that SVs were the lead variant for ~70% of loci!!!!

Getting excited for #ASHG25. The must see talk is tomorrow at 1:30 by Qiuhui (Iris) Li presenting the first large-scale integration of long-read genome sequencing with electronic health record data across >1000 All of Us participants meetings.ashg.org/event/ASHG25...

Postdoc Description.docx Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

Xcode is the Worst Piece of Professional Software I Have Ever Used | Hold The Robot The compiler is unable to type-check this expression in reasonable time; try breaking up the expression into distinct sub-expressions

After vibe coding a little swift this summer, I feel totally validated by this post! holdtherobot.com/blog/xcode-i...

Easy! We dont we change the USA to the metric system too while we are at it!

zcat reads.fq | paste - - - - | awk '{print $2}'

This is amazing

overview

after a long effort, gathering a lot of input from many people, we finaly put it all together:
Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)
https://www.preprints.org/manuscript/202509.0823
Thank you very much to all people involved !

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...

GTN is now integrated with WorkflowHub Thanks to a collaborative effort between the teams at Galaxy Training Network (GTN), WorkflowHub, and Australian BioCommons, GTN workflows are now registered automatically with WorkflowHub. The existi...

🎉 Big news! Galaxy Training Network workflows are now automatically registered on WorkflowHub.
Easier discovery, citation, & direct Galaxy execution → boosting FAIR & accessible training!

training.galaxyproject.org/training-mat...

I dont think this is totally up to date, but I bet this still generally reflects the overall distribution in capacity: enseqlopedia.com/ngs-mapped/

Big Data: Astronomical or Genomical? This perspective considers the growth of genomics over the next ten years and assesses the computational needs that we will face relative to other "Big Data" activities such as astronomy, YouTube, and...

Ten trillion years ago we tried to track this down from and predicted we should be about exabyte range now, but I have not tried to revise this estimate since. journals.plos.org/plosbiology/...

My strong belief is there is much more sequencing going on in private companies (especially diagnostics) than academic work so just looking at SRA/ENA will substantially undercount

This is a hard number to track. Illumina, PacBio, & ONT are publicly traded companies so you can get an estimate of instruments & reagents sold from their disclosures, but that doesnt mean they are actively being used by their customers at full capacity.

Please repost!

We have an open rank, tenure-line faculty position in biomechanics in the School of Kinesiology at the University of Michigan Ann Arbor. At U-M we have great colleagues, exceptional resources, and biomechanics can be found all across the campus. #BiomechSky

JXTX + CSHL 2025 Genome Informatics Scholarship JXTX + CSHL 2025 Genome Informatics Scholarships

Scholarships available for Genome Informatics - just include a brief summary on your open science work plus your conference abstract. If you have already paid to register, we will work with CSHL to refund you the $$$. Apply today! jxtxfoundation.org/news/2025-6-... @jxtxfoundation.bsky.social

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

📢🚨📢🚨 Genome Informatics deadline extended to September 8! meetings.cshl.edu/meetings.asp....
Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!

Genome Informatics abstract deadline now Sept 8! h/t @benlangmead.bsky.social meetings.cshl.edu/meetings.asp...

Checking out the new JHU student center! Super impressive inside! @jhu.edu

Researchers build a smarter tool for reading genetic code The Hopkins team’s new, open-source software dramatically improves scientists’ ability to detect genetic modifications that control gene activity.

Johns Hopkins researchers including @mikeschatz.bsky.social & @vikramshivakumar.bsky.social have developed Uncalled4, a new software toolkit that can detect epigenetic changes—chemical modifications to normal DNA and RNA that control which genes are turned off and on—with unprecedented accuracy.

🎉 Galaxy has passed 21,000 citations on Google Scholar!
A huge thank you to the global community of researchers who use and advance Galaxy for open, reproducible science.

Amazing line up! So sad to miss it

This popped up in my feed today: adele.pollux.casa/gemlog/2025-...

Just started! openai.com/live/

Individual academics probably don’t have enough clout to apply any real pressure although if we band together we maybe do. This could be a good topic for GA4GH or another society to address

Another dimension to this is when code should be directly interacting with files vs leveraging an API. As datasets get increasingly large I see API based access becoming more popular, especially for data in the cloud

And as much as I hate fastq, at least it doesnt have vendor lock in. As recently as yesterday I was fighting with cbcl files that could only be converted by bcl-convert (closed source/closed binary from Illumina)

The Sequence Alignment/Map format and SAMtools Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by diff...

But in this spirit if we see "specialized" code being stretched into "production" use, then we should encourage the development of harden tools and formats to use and work with it. This can also be incredibly successful as a publication, e.g. SAMTools has been cited 60k times