Torsten Seemann

2500 prokkas oh no.

``` space Delete most of the unnecessary big files panic In case of emergency only! More help: https://github.com/tseemann/nullarbor#nullarbor tseemann@trillian:nullarbor $ make space make: *** No rule to make target 'space'....

eg. use `spades.fa` first, then `skesa.fa` etc

Useful for when you just want the tree quickly.

Maybe need to delete some files OR Depend on `isolates.txt` somewhere? OR delete `report/` also affecting `roary_NNNNNNNN` if `roary` exists already

Can't do it if it is a FNA though

`--metadata` will take a TSV with Column Headers. must have column `ID` for isolate Rest a free form and will be added to the report and tree (somehow)

Put each CDS in a fake contig. See https://github.com/sanger-pathogens/Roary/issues/395

Don't allow dashes in IDs to wrap in SNP table

1


This will make clusters much easier to see.