Running nullarbor.pl on assembled genomes

[com31]

How can we run the nullarbor.pl with assembly option switched off? This may come handy when analysing already assembled genomes available in public databases.

[tseemann]

There is no way to do this in Nuillarbor, sorry.
It is planned however.

We do have a --prefill option which we use here, to re-use existing assemblies.
https://github.com/tseemann/nullarbor#prefilling-data
You still need reads however.

The underlying Snippy tool has a special wrapper called snippy-multi which allows PE reads and Contigs in it's input file. But it only does the phylo tree and nothing else.

https://github.com/tseemann/snippy#using-snippy-multi

Other options may be to see if Bohra supports what you desire:
https://github.com/kristyhoran/bohra