Contact

Bugs, questions, feature requests

Please open a GitHub issue. It helps enormously to include:

• the exact command or code you ran

• the full traceback

• how you obtained the weights (data/download.sh, direct link, retrained)

• your OS, Python, and TensorFlow versions

Other inquiries

• David R. Kelley — drk (at) calicolabs.com

• Johannes Linder — jlinder (at) calicolabs.com

• Kuan-Hao Chao — kuanhao.chao (at) gmail.com

Links

• Code: https://github.com/calico/shorkie-paper

• Documentation: https://khchao.com/shorkie/

• Preprint: https://doi.org/10.1101/2025.09.19.677475

• Model framework: baskerville-yeast · westminster

Other tools from the same author

• LiftOn — genome annotation lift-over

• OpenSpliceAI — splice-site prediction

• splam — splice-junction scoring