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Plant-Food-Research-Open / genepal

A Nextflow pipeline for genome and pan-genome annotation
https://github.com/Plant-Food-Research-Open/genepal/blob/main/docs/README.md
MIT License
8 stars 2 forks source link

Lifton vs Liftoff #76

Open annabel-NZ opened 3 weeks ago

annabel-NZ commented 3 weeks ago

Description of feature

Hi Jason, This workflow looks great and I hope to try it out soon. If you haven't already considered it, you might want to take a look at incorporating this tool as an alternative/replacement for LiftOff. I particularly like the feature it has to annotate the identity/variation type relative to the source annotation. https://github.com/Kuanhao-Chao/LiftOn Kua-Hao Chao, Jakob M. Heinz, Celine Hoh, Alan Mao, Alaina Shumate, Mihaela Pertea, and Steven L. Salzberg. "Combining DNA and protein alignments to improve genome annotation with LiftOn." bioRxiv, doi: https://doi.org/10.1101/2024.05.16.593026, 2024.

GallVp commented 3 weeks ago

Hello @annabel-NZ

Thank you for the suggestion. We have considered it and will incorporate in a future release.