2024-hpc-sourmash-example

An example of using sourmash on the HPC, with options for parallelism etc.

Quickstart

Start in a local clone of the git repo:

git clone https://github.com/ngs-docs/2024-hpc-sourmash-example
cd 2024-hpc-sourmash-example

Install the necessary software via conda:

conda env create -n smash -f environment.yml

Activate the conda environment and sketch the genomes:

conda activate smash
sourmash sketch dna data/*.fa

Now run your commands, like so:

sourmash scripts manysearch 1.fa.sig /group/ctbrowngrp/sourmash-db/gtdb-rs214/gtdb-rs214-reps.k31.zip -o 1.csv -c 4

Note that this uses the GTDB rs214 reps database from the sourmash databases page.