LiftClean detects issues in lifted-over annotations that conflict with coding gene models
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LiftClean Docker Hub
GitHub - LiftClean GitHub
README - LiftClean documentation
LiftClean execution
# From Linux:
docker run --rm -it -v "$(pwd)":/data -w /data gemygk/liftclean:v0.2.0 liftclean -h
# From Mac OS (If you’re on an Intel Mac, you can omit --platform linux/amd64.)
docker run --platform linux/amd64 --rm -it -v "$(pwd)":/data -w /data gemygk/liftclean:v0.2.0 liftclean -h
# From Windows PowerShell:
docker run --rm -it -v "${PWD}:/data" -w /data gemygk/liftclean:v0.2.0 liftclean -h
apptainer exec docker://gemygk/liftclean:v0.2.0 liftclean -h
singularity exec docker://gemygk/liftclean:v0.2.0 liftclean -h
# If you need to mount a specific directory
apptainer exec --bind "$PWD":/data --pwd /data docker://gemygk/liftclean:v0.2.0 liftclean -h
singularity exec --bind "$PWD":/data --pwd /data docker://gemygk/liftclean:v0.2.0 liftclean -h
Tools installed in the instance
⚠️ Disclaimer The dependencies for these tools were installed directly into the Docker image, and not all dependencies are listed here. For any third-party files or components, the original licenses provided by their respective authors apply.
Citing LiftClean
Kaithakottil, G., & Swarbreck, D. (2026). EI-CoreBioinformatics/LiftClean: v0.2.0 (v0.2.0). Zenodo. https://doi.org/10.5281/zenodo.20810870
Content type
Image
Digest
sha256:c53b44927…
Size
1.9 GB
Last updated
3 months ago
docker pull gemygk/liftclean:v0.2.0