1.JupiterPlot下载地址：https://github.com/JustinChu/JupiterPlot
一种基于Circos的工具，与参考基因组相比，可以可视化基因组组装的一致性。依赖软件circos，minimap2 ，samtools。
2.JupiterPlot安装
直接github 下载，下载方式很多，下载解压即可。
接着需要将minimap2加入当前环境：
export PATH=/share/nas2/genome/biosoft/minimap2/current/:$PATH
3.参考命令如下：
分析前，建议提取两个物种染色体序列进行比较画图。
export PATH=/share/nas2/genome/biosoft/minimap2/current/:$PATH
export PATH=/share/nas2/genome/biosoft/circos/circos-0.69/bin/:$PATH
reference=Chr.ref.fa
scaffolds=Chr.query.fa
/share/nas1/user/01.software/JupiterPlot/JupiterPlot-master/jupiter name=test ref=$reference fa=$scaffolds labels=both
主要使用的参数说明：
name 输出文件前缀
ref 参考基因组，写的时候在前面
fa 自己的物种基因组，写的时候再后面
labels=both 表示显示ref 和fa两者的染色体id
4.使用中可能存在的问题：
如果使用过程中发现id不全，需要在日志文件nohup.out中一步步debug，手动调整整理好。例如需要加上-g 10000，ref 的染色体id才会抓全。
nohup.out中:
perl /share/nas1/user/01.software/JupiterPlot/JupiterPlot-master/bin/generateConf.pl -n 200 -m -1 -r /share/nas1/user/01.software/JupiterPlot/JupiterPlot-master/config/rawConf.conf -p test -s test_scaffolds.fa -b test-agp.bed -a test.agp -k test_reference.karyotype -g 100000
Optional commands:
sam= #Specify an existing alignment of scafftigs to if they already exist (naming convention that fatoagp.pl produces must be consistent)
######General Parameters
t=4 #number of threads to use for minimap2
>######Karyotype options
m=100000 #only use genomic reference chromosomes larger than this value
ng=75 #use largest scaffolds that are equal to 75% of the genome
maxScaff=-1 #Instead of ng filter by this number of scaffolds
i=0 #increment for colouring chromosomes (HSV colour shift by setting 0-360), when set to >360 it generates random colours
g=1 #minimum gap size in reference to render
gScaff=100000 #minimum gap size in scaffolds to render
labels = ref #Shows reference chromosome name "ref", scaffolds "scaf" or "both".
######Link options
maxGap=100000 #maximum alignment gap allowed to consider a region contiguous
minBundleSize=50000 #minimum size of a contiguous region to render
MAPQ=50 #maximum mapping quality allowed when filtering
linkAlpha=5 #alpha of links 1 = 17% , 2 = 33%, 3 = 50%, 4 = 67% and 5 = 83%.
结果如下：
image.png
5.结果调整
1.同时显示两者的染色体id需要注释掉配置文件
#注释掉test.conf中的label_format = eval( var(chr) =~ /scaf(\d+)$/ ? "": var(label) )
#radius = 0.80r #染色体id太多，调小半径
