Processing of public metagenomic data that has been analysed with SingleM.

Most code here is not intended for public usage as many paths etc are specific to CMR / QUT / Woodcroft group, but nonetheless may be useful for others.

Post-processing a singlem renew run of SRA data

First modify paths at the top of the Snakemake

Then setup:

mamba env create -p env_singlem_sra_processing -f env.yml
conda activate ./env_singlem_sra_processing

and run

snakemake --use-conda --cores 1

Make sure the correct taxonomic level is chosen for applying predictions in the Snakemake file. See {base_output_directory}/logs/host_or_not_prediction.log for the results of the cross validation.

Host-vs-not metagenome prediction

Example code for host-vs-not prediction is contained within the Snakefile. In