quartet补gap

conda create -n quarTeT python=3.7.4 MUMmer4 tidk=0.2.1 gnuplot=4.6.0 Minimap2=2.24

##Python3 (>3.6, tested on 3.7.4 and 3.9.12)
##Minimap2 (tested on 2.24-r1122 and 2.24-r1155-dirty)
##MUMmer4 (tested on 4.0.0rc1)
##trf (tested on 4.09)
##CD-hit (tested on 4.6 and 4.8.1)
##BLAST+ (tested on 2.8.1 and 2.11.0)
##tidk (<0.2.31(not include), tested on 0.2.1)
##gnuplot (tested on 4.6 patchlevel 2 and 6)
##R (tested on 3.6.0)
##RIdeogram (tested on 0.2.2)

##quarTeT.sh
#!/usr/bin/bash
genome=/home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/final_assembly_descending.fa  ##juicer调整之后的结果
contig=/home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/BMK220921-BB398-02P0001/cell/BMK220921-BB398-02P0001.ccs.fasta ##可以是ccs reads, 也可以是组装好的contig
export PATH=/home/lx_sky6/software/soft/miniconda3/bin:$PATH ##trf 
export PATH=/home/lx_sky6/software/miniconda3/envs/quarTeT/bin:$PATH ##Python3 Minimap2 MUMmer4 tidk gnuplot blast+ cd-hit
python /home/lx_sky6/yt/soft/quarTeT/quartet.py  GapFiller  -d  $genome -g $contig -t 40 --minimapoption \'-x map-hifi\'


bash quarTeT.sh


##或者
conda activate quarTeT
python /home/lx_sky6/yt/soft/quarTeT/quartet.py  GapFiller  -d  /home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/final_assembly_descending.fa  -g /home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/BMK220921-BB398-02P0001/cell/BMK220921-BB398-02P0001.ccs.fasta -t 30 --minimapoption \'-x map-hifi\'