search

aaranyue / quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
http://atcgn.com:8080/quarTeT/home.html
101 stars 7 forks source link

How to fill genome gaps using quarTeT software for ONT data #38

Open Apl-cc opened 2 months ago

Apl-cc commented 2 months ago

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 commented 2 months ago

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