The --external-mums flag lets you bypass parsnp's internal MUM search entirely and instead use precomputed MUM locations from mumemto.
For general instructions on running parsnp, check out https://github.com/marbl/parsnp. To use the --external-mums flag, clone this repo into your local repository. To compile, follow the instructions on the normal parsnp2 repository linked above. Make sure you are in the correct directory with the parsnp file, and then use the following command :
./parsnp -r <reference.fna> -d <genomes/> --external-mums <output.mums> --mum-length 10000000 --no-partition --skip-phylogeny --skip-ani-filter
The .mums file must be the direct output of mumemto. The .lengths file (automatically generated by mumemto), with the same base name must exist in the same directory. For more information on mumemto output, see https://github.com/vikshiv/mumemto/
These flags should be used when using the --external-mums flag.
--mum-length 10000000 : skip internal recursive mum search.
--no-partition : External MUMs are not compatible with partition mode
--skip-phylogeny, --skip-ani-filter : Recommended for compatibility