README

To run

Remove adapters and demultiplex fastq files.

bash trim.sh -f /path/to/fastqs.gz -t threads -r results

Get spikein counts for each sample.

bash get-counts.sh

Get plots.

Rscript plot.R

To use Snakemake

Install using:

pip install snakemake

This will run the Snakefile in the current directory. To run with additional cores, use:

snakemake --cores [number_of_cores]

Use Snakemake with Apptainer

I have an apptainer image put together, which may be more streamlined for you rather than installing the dependencies yourself.

First make sure you have [apptainer]. Then run:

apptainer build spikein-analysis.sif Apptainer