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nf-LO

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

Install

See here for instructions on how to install the software and/or its dependencies.

The workflow

The workflow consists of four major steps:

1. Chunking of the genomes: not always needed, but can 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 get you up and running with nf-LO!

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

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

See the custom configurations section for how to run the workflow on your local system.