---
name: "mash2matrix"
section: "1"
platform: "linux"
package: "seer"
version: "1.1.4-8+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mash2matrix"
---

# mash2matrix(1)

create all pairwise distances between samples

## 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.