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nf-LO

nf-LO is a nextflow pipeline to generate lift over chain/net files for any pair of genomes.

The workflow consists of four major steps:

1. Chunking of the genomes: not always needed, but speed up the work!
2. Alignment: this step can be performed using different aligners; fine tuning it can greatly improve the results
3. Chain/netting: generation of the chain/net for the liftover
4. Lift the positions: if a file is specified, it will be automatically lifted (if possible)

If you have a couple of genomes that you want to process, you can simply follow our step-by-step guide, which will put you up and running with nf-LO!

If you want more control over the workflow, and try to improve your newly generated chain/net files, simply follow the sub-sections below:

1. Inputs
2. Alignments
3. Chain/Net
4. Liftover