README.md

ONT_polish

The script ONT_polish.sh takes a Nanopore assembly and runs four rounds of Racon polishing using MiniMap2 for read mapping, and then one round of Medaka polishing.

Dependencies

Minimap2 GitHub page and Conda install

Racon GitHub page and Conda install

Medaka GitHub page and Conda install

Usage

usage: ./ONT_polish.sh -a <assembled contigs as fasta> -r <Nanopore reads as fastq> [optional arguments]

Mandatory arguments:
    -a : assembled contigs as fasta file
    -r : Nanopore reads as fastq (or fastq.gz) file
    
Optional arguments:
    -m : Medaka model | default: r941_min_hac_g507
    -t : number of CPUs | default: 1
    -o : output directory | default: current directory