Step-by-step example

nf-LO is a workflow that generates chain/net files for any two pairs of genomes. These genomes can be either local or remote (the latter provided as an ftp address, iGenome ID or RefSeq/GenBank accession from NCBI).

Installation

First, check you have all you need to run nf-LO. If you’re in a hurry, just install nextflow and anaconda: you’re ready to go! If you need more control, or you can’t run anaconda, follow the installation section to find the best solution for you.

Premise

Before running nextflow, you have to decide what type of workflow you want to use. This depends on whether you are processing genomes of the same species, or of different species, and how closely related they are. The choice is ultimately yours; in general, we recommend the following:

• same species liftover: blat and GSAlign

• different species liftover: lastz and minimap2

We also provide a series of pre-defined configurations. These are described in the alignments and chaining pages of the wiki.

Run the workflow

Once defined the type of aligner you want to use and the distance among your genomes, you can simply run nf-LO as follow:

nextflow run evotools/nf-LO --source mygenome1.fa --target mygenome2.fa --distance near --aligner lastz --outdir ./liftover_genome1_genome2 --no_netsynt -profile conda 

The workflow will pre-process the inputs and return the results in the folder specified. The content is better described in the output section.