GitHub - jheinz27/breakinator: Tool to flag foldback and chimeric artifacts in long-read sequence alignment files Tool to flag foldback and chimeric artifacts in long-read sequence alignment files - jheinz27/breakinator

Breakinator: github.com/jheinz27/bre...

Detecting foldback artifacts in long-reads - BMC Genomics Long-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of ...

Our paper on foldback artifacts in long-read sequencing is now published in BMC Genomics!

We introduce Breakinator to flag foldback and chimeric artifacts across library types, sequencers, and chemistries.

Paper: link.springer.com/article/10.1...

With Matthew Meyerson and @lh3lh3.bsky.social

If you’re in Liverpool, stop by my poster A217 at ISMB/EECB 2025, and chat about all things pangenomes, MUMs, and alignment (and the Beatles or Oasis-mania)

Excited to share our new preprint on detecting foldback artifacts in long reads with my advisors Matthew Meyerson and @lh3lh3.bsky.social ! Stop by poster C-180 on Wednesday at ISMB/ECCB2025 to learn more and chat!

Our pre-print on investigating variation in South Asian genomes is now out!

Thank you to @mikeschatz.bsky.social, @rajivmccoy.bsky.social and @aabiddanda.bsky.social for all their work on this.

🧵 A thread on the key results and takeaways from our work:

Friends, LiftOn is now published in @genomeresearch.bsky.social! LiftOn maps genes across genomes using a protein-centric, homology-based approach with both DNA & protein alignments
@stevensalzberg.bsky.social Mihaela Pertea, Jakob Heinz, Alaina Shumate, Celine Hoh, Alan Mao
doi.org/10.1101/gr.2...