5  A Checkout Challenge

If you’re looking for a task to do in snakemake why not try this experiment on the TSL cluster.

On TSL’s sequence database we have this Arabidopsis project. It contains six samples and two run files per sample. Write a snakemake pipeline to

1. QC the reads with e.g fastqc
2. Find SNPs with e.g vcftools
3. Estimate read counts/TPM with e.g kallisto

Happy snakemake-ing.