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MASH2MATRIX(1) User Commands MASH2MATRIX(1)

NAME

mash2matrix - create all pairwise distances between samples

SYNOPSIS

mash2matrix <matrix_in> > all_distances.csv

DESCRIPTION

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

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
March 2017 mash2matrix 1.1.2