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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)

See the separate subsections for further details:

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