MASH2MATRIX(1)

🌸 NAME 🌸

mash2matrix — bestie, it creates all pairwise distances between samples. every single one. no crumbs left. 💅

✨ SYNOPSIS ✨

mash2matrix <matrix_in> > all_distances.csv

okay so you feed it a matrix and it screams a csv of every distance back at you. iconic behaviour honestly.

🦋 DESCRIPTION 🦋

It uses mash (<http://mash.readthedocs.io/> — that's the link, go look, i'm not gonna gatekeep) to create all pairwise distances between samples. all of them. the whole friend group gets compared to the whole friend group. 🫶

NB: the input to mash has to be in the same order as the .pheno file. same order, bestie, i cannot stress this enough. 🙈

to generate <assemblies.fa> you do this:

cut -f 1 metadata.pheno | tr '

' ' '

(yes the line break inside the quotes is literally in the original. that's just how it's written. 💀)

then you run:

mash sketch -o reference <assemblies.fa>

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

mash2matrix mash_distances.txt > all_distances.csv

and boom, all_distances.csv is yours. slay. ✨

💖 AUTHOR 💖

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. shoutout to Andreas fr fr, the manpage ate and left no crumbs. 👑

and that's the whole page, bestie 🎀 — this was mash2matrix version 1.1.2, dating all the way back to March 2017, and you've been reading the User Commands manual. mwah, go compute some distances. 💜🦋