Everything is still bigger in Texas: The 8th Pan-Structural Variation Hackathon in the Cloud!

The Structural Variants in the Cloud Hackathon returns in 2026, bringing together the structural variation community for another round of collaborative, hands-on bioinformatics research. After years of building tools, workflows, benchmarks, and publications through this hackathon series, we are excited to continue the momentum and welcome new ideas, new participants, and new challenges.

Baylor College of Medicine, together with Rice University, will host this hybrid bioinformatics hackathon in collaboration with GREGOR and SMAHT consortia. With support from friends at NCBI and the broader genomics community, this event will bring together researchers, students, developers, and data scientists who are interested in solving real-world challenges in structural variant (SV) analysis — whether joining in person or virtually over Zoom.

This year, we will again focus on open, team-based projects that push the boundaries of SV discovery, annotation, benchmarking, visualization, and interpretation across large-scale genomic datasets. Participants will work collaboratively, exchange expertise, and develop practical resources that can benefit the broader genomics community.

🗓️ Mark your calendars: August 25–28, 2026 — don’t miss this opportunity to collaborate, learn, and advance SV research together!

🧬 Topics we might explore this year include:

Long-read Methylation!
SV annotation using pan-genome and graph-based references
Novel approaches for benchmarking SV callers across diverse populations
Large-scale SV curation and visualization
SV impacts on transcript structure and splicing
Integration of SVs in rare disease diagnostics pipelines
Mobile element insertions in population-scale datasets
Exploring long-read metagenomic assembly for SV discovery
Mosaic/Somatic variant detection
Assembly annotation and pan-genome-based approaches for enhancing variant calling accuracy

Got another idea? We’re always open to bold and creative proposals that push the boundaries of SV research!

🫵 How to Apply

📝 Applications are due by 10th of Aug via here

💻 Basic scripting knowledge (e.g., Shell, Python, R) is helpful but not required.

We can’t wait to see what ideas you bring to the table! If you have any questions, feel free to reach out to Ben Busby or Fritz Sedlazeck via fritz.sedlazeck@bcm.edu.

🌍 Where in the world are our hackathon participants from?

This map shows the incredible global reach of our past Structural Variation Hackathons — participants have joined us from across North America, Europe, Asia, and beyond! Whether dialing in from bustling research centers or quiet home offices, our community proves that impactful science knows no borders. We can’t wait to see where this year’s attendees will be joining from!

🧑‍🎓 Who Should Apply

We’re looking for motivated individuals with experience in genomics, bioinformatics, structural variation, or related fields. Whether you’re a graduate student, postdoc, data scientist, or software developer, if you’re interested in complex variation, genome graphs, precision medicine, or building pipelines on the cloud — this hackathon is for you!

This is a collaborative event, not a competition. You’ll join a team of 5–6 participants and work together on a real, open-ended bioinformatics project. Teams will have access to cloud-based computing resources, support from experts in the field, and lots of caffeine-fueled inspiration.

🧰 Products & Publications

All code, pipelines, and scripts developed during the hackathon will be shared publicly via the Collaborative Bioinformatics GitHub. Teams will also be encouraged to submit manuscripts describing their work to outlets such as F1000Research (Hackathons Channel), BMC Bioinformatics, GigaScience, Genome Research, or PLOS Computational Biology.

Check out our previous publications!

🏗️ Organization & Format

After a brief kickoff and organizational session, teams will spend four full days tackling a challenging set of problems related to structural variation and large-scale datasets. Teams will analyze and integrate public datasets, share insights, and collaborate in a highly interactive environment. Throughout the event, we’ll also gather to discuss progress, best practices in bioinformatics, coding standards, and more.

On the final day, each team will give a short presentation on their work. The top two teams will receive special prizes sponsored by Oxford Nanopore Technologies and Pacific Biosciences!

💻 How It Works

Selected applicants will be assigned to project teams before the event begins. Projects will be announced shortly before the hackathon kicks off, and will build upon ideas from previous NCBI-style hackathons, community initiatives, and ongoing genomics challenges.

The event runs across four full days, so please make sure you’re able to commit to the entire duration. No registration fees. Just bring your brain, your laptop, and your curiosity.

SV Hackathon 2026