「基因组」JupiterPlot评估基因组

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。

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

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

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：