A simple Snakemake workflow for preprocessing of ONT (Nanopore) raw reads.
Currently designed to:
a) Quality filter using nanoq
b) Subsample using seqtk
c) Trim adapters using porechop
d) Generate a summary report using nanoq
Minimum read length, quality, and subsampling depth are currently set to 500bp, 12, and 60,000, respectively. Values can be adjusted directly in the Snakefile for variable processing.
Suggested usage:
- Clone repo to desired workspace.
- Create conda environment using provided environment file.
- Run workflow by activating Snakemake with the desired number of
--cores