sourmash-slainte

sourmash-slainte is a snakemake workflow that takes in a collection of metagenomes and (optionally) a set of genome sequences (e.g. reference genomes, isolates, SAGs, or MAGs). It then performs a number of default comparisons. sourmash-slainte is intended to be a good starting template for projects that need to work with many large metagenomes.

The current list of default analyses (Jan 2024) is:

• all-by-all comparison of metagenomes
• all-by-all comparison of genomes
• genome detection within metagenomes
• genomic composition of metagenomes & associated taxonomy

Quickstart

Allocate computational resources, here 128 CPUs and 120 GB of RAM for 3 days via Slurm:

srun -p high2 --time=72:00:00 --nodes=1 --cpus-per-task 128 --mem 120GB --pty /bin/bash

Create a conda environment with the necessary software:

mamba env create -n slainte -f environment.yml 

Run!

snakemake --cores 128 --resources gather=2 -k

CTB to add:

• some minimal configuration!
• estimate ~20 GB per gather?
• n.b. fastgather doesn't use more memory with threads