How to fill genome gaps using quarTeT software for ONT data

[Apl-cc]

source /home/anpl/miniconda3/bin/activate

conda activate quartet

/home/anpl/miniconda3/bin/python /home/anpl/01.soft/quarTeT/quartet.py GapFiller -d ./Tmono_v2.rename.sorted.fa -g ./ont.fasta -t 40 --minimapoption '-x map-ont'

or
/home/anpl/miniconda3/bin/python /home/anpl/01.soft/quarTeT/quartet.py GapFiller -d ./Tmono_v2.rename.sorted.fa -g ./ont.fasta -t 40

[Echoring]

Default minimap paramater is -x asm5. If ONT data has ben assembled to contig level, use default, else use --minimapoption '-x map-ont'.