Hello! This repository contains short and simple tutorial to start with for Fiber-seq data processing. It is supplementary material to Multiomics workshop given at LRUA 2026.
We use publicly available data, downsample it and demonstrate how to run a few simple fibertools commands and how to interpret their output.
You can find slides from the session here: #TODO add slide link (PDF hosted here)
In case of questions about this workshop, feel free to open an issue or get in touch @ alexandra.pancikova[at]kuleuven.be
Majority of the tutorial relies on tools and data produced by the lab of Andrew Stergachis. Please cite relevant publications when using the data or tools
Fiber-seq method
Stergachis AB et al. Single-molecule regulatory architectures captured by chromatin fiber sequencing. Science 2020. 368(6498):1449-1454. DOI: 10.1126/science.aaz1646
Fibertools
Jha, A., Bohaczuk, S. C., Mao, Y., Ranchalis, J., Mallory, B. J., Min, A. T., Hamm, M. O., Swanson, E., Dubocanin, D., Finkbeiner, C., Li, T., Whittington, D., Noble, W. S., Stergachis, A. B., & Vollger, M. R. (2024). DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools. Genome Research. https://doi.org/10.1101/gr.279095.124
FIRE elements
Vollger, M. R., Swanson, E. G., Neph, S. J., Mallory, B. J., Dubocanin, D., Ho, C.-H., Cheng, Y.-H. H., Ranchalis, J., Munson, K. M., Sedeno-Cortes, A. E., Mudeppa, D. G., Fondrie, W. E., Bohaczuk, S. C., Dippel, M. A., Mao, Y., Parmalee, N. L., Harvey, W. T., Kwon, Y., Garcia, G. H., Hoekzema, K., Meyer, J. G., Cicek, M., Eichler, E. E., Noble, W. S., Witten, D. M., Bennett, J. T., Ray, J. P., & Stergachis, A. B. (2026). Somatic epimutations cap genetic determinism in the human diploid chromatin epigenome. Cell, 189(21), 6613-6629.e9. https://doi.org/10.1016/j.cell.2026.09.034
HPRCv2 data
Julian K. Lucas, Prajna Hebbar, Wen-Wei Liao, ... Adam M. Phillippy, Ting Wang, Benedict Paten (2026). HPRC2: A human pangenome reference with near-complete coverage of common genetic variation. bioRxiv. https://doi.org/10.64898/2026.07.21.739710
Claude has been used to tidy up the documentation to this tutorial.