- intersect pairwise genome alignment results in UCSC chain format (obtained for instance using cactus: https://github.com/ComparativeGenomicsToolkit/cactus) for different species, two being typically refs and others outgroups, in order to obtain common sections
- get ancestral genome for refs using outgroups
- analyse pattern of mutations in regions of interest, here NIEBs.
- snakemake
- bedtools
- R
- Python 3
- cmake
- compiler compatible with C++ 17
Clone the git repo and then issue the snakemake command. You must specify number of cores to use through the -nx (with x being the quantity of cores) or --cores x. The pipeline has only like 8 steps that can be launched in parallel so no need to specify more (they won't be used).
You can get to a particular step of the pipeline by calling its name or its output : for instance :
- if you want the bed with all the common regions between outgroups, you need to call
snakemake -n1 data/intersected.bed - for the ancestral genomes just call the full pipeline.