导读

用MUMmer，做比较基因组，比对完后用mummerplot做可视化踩了三个坑。MUMmer软件包中五个常用的程序：mummer, nucmer, promer, run-mummer1, run-mummer3。各版本的MUMmer3/4比对哺乳动物基因组也很OK。NUCmer3文档提到适合比对closely related基因组。

文献：这是老牌软件

MUMmer 1.0
Alignment of Whole Genomes. Nucleic Acids Research 1999
MUMmer 2.1, NUCmer, and PROmer
Fast Algorithms for Large-scale Genome Alignment and Comparision. Nucleic Acids Research 2002
MUMmer 3.0
Versatile and open software for comparing large genomes. Genome Biology 2004
MUMmer4
A fast and versatile genome alignment system. PLoS Comput Biol. 2018

软件地址

MUMmer4官网：https://mummer4.github.io/
MUMmer4 Github：https://github.com/mummer4/mummer
sourceforge: http://mummer.sourceforge.net/
Manual: http://mummer.sourceforge.net/examples/
MUMmer3 manual: http://mummer.sourceforge.net/manual/

软件获取

conda install mummer
mummer -h

里面的主程序

NUCmer比较两个基因组

从ncbi taxonomy -> genome下载的两个梭菌complete基因组

nucmer --mum -p test_nucmer -t 2 Clostridium_beijerinckii.fna Clostridium_botulinum.fna

生成比对结果文件：test_nucmer.delta

MUMmerplot可视化

mummerplot坑一

运行出现两个warning

mummerplot -p test_plot test_nucmer.delta

gnuplot 5.0 patchlevel 3
Reading delta file test_nucmer.delta
Writing plot files test_plot.fplot, test_plot.rplot
Writing gnuplot script test_plot.gp
Forking mouse listener
Rendering plot to screen
WARNING: Unable to query clipboard with xclip
WARNING: Unable to run 'false -geometry 500x500+0+0 -title mummerplot test_plot.gp', Iriate ioctl for device

解决方案：删除mummerplot文件中含clipbord的行
参考：https://github.com/mummer4/mummer/issues/9

mummerplot坑二

第二个warning还在

mummerplot -p test_plot test_nucmer.delta

gnuplot 5.0 patchlevel 3
Reading delta file test_nucmer.delta
Writing plot files test_plot.fplot, test_plot.rplot
Writing gnuplot script test_plot.gp
Forking mouse listener
Rendering plot to screen
WARNING: Unable to run 'false -geometry 500x500+0+0 -title mummerplot test_plot.gp', Iriate ioctl for device

解决方案：mummerplot文件中：$GNUPLOT_EXE="false" 改成 "gnuplot"
参考：https://github.com/mummer4/mummer/issues/36

mummerplot坑三

其实就是需要图形化界面，没有啊

mummerplot -p test_plot test_nucmer.delta

gnuplot 5.0 patchlevel 3
Reading delta file test_nucmer.delta
Writing plot files test_plot.fplot, test_plot.rplot
Writing gnuplot script test_plot.gp
Forking mouse listener
Rendering plot to screen
WARNING: Unable to query clipboard with xclip gnuplot: unable to open display 'localhost:10.0' gnuplot: X11 aborted.

解决方案：添加参数”--png“

mummerplot --png -p test_plot test_nucmer.delta
convert -quality 200 -density 400 test_plot.png test_plot.pdf

更多
MUMMER 两个基因组间比较
MUMmer共线性分析与SNP检测
Viral-genome-assembly

How to covert snp file from MUMmer into VCF format
vcf似乎可将多个结果合并
生物信息百Jia软件（九）：Mummer