ONTPreProcess

A workflow for preprocessing of ONT (Nanopore) raw reads.

Currently designed to:

a) Quality filter using nanoq
b) Remove host reads using mimimap2
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 300bp, Q=12, and 60,000 reads, respectively. Values can be adjusted directly in the Snakefile for variable processing. For the removal of host reads, the workflow assumes a local directory refs with a refs/host.fasta file present.

Suggested usage:

1. Clone repo to desired workspace.
2. Create conda environment using provided environment file.
3. Run workflow by activating Snakemake with the desired number of --cores