mash2matrix

mash2matrix <matrix_in> > all_distances.csv

Uses mash (http://mash.readthedocs.io/) to create all pairwise distances between samples.

NB: the input to mash should be the same order as the .pheno file generate <assemblies.fa> with:

cut -f 1 metadata.pheno | tr '

' ' '

Then run

mash sketch -o reference <assemblies.fa>

mash dist reference.msh reference.msh > mash_distances.txt

mash2matrix mash_distances.txt > all_distances.csv

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.