Centromics 软件鉴定可能的着丝粒区域

我是在草莓的T2T文章里看到的这个软件

The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry

Centromics software (https://github.com/ShuaiNIEgithub/Centromics) was used to identify centromeres

这个软件还没有对应的论文

论文正文中只用了一个表格展示着丝粒的位置，论文里写了还有一个补充图对应的是着丝粒的结果，但是补充文件里只有一个word文档，并没有对应的图片和表格。

https://github.com/zhangrengang/Centromics/tree/master

直接按照软件的github主页的帮助文档进行安装就可以

我用草莓的hifi数据加组装数据试了试

centromics -l ../hifi/SRR22495382_subreads.fastq.gz -g ../galba.genome.annotation/fv.fna -p 48

中间遇到报错

24-03-13 17:15:20 [INFO] run CMD: cd /data/myan/raw_data/practice/strawberry/RepCent.practice/cent-output/centomics.circos && circos -conf ./circos.confTraceback (most recent call last): File "/home/myan/anaconda3/envs/RepCent/lib/python3.8/shutil.py", line 791, in move os.rename(src, real_dst) FileNotFoundError: [Errno 2] No such file or directory: '/data/myan/raw_data/practice/strawberry/RepCent.practice/cent-output/centomics.circos/circos.svg' -> '/data/myan/raw_data/practice/strawberry/RepCent.practice/cent-output/centomics.circos/circos.svg.bk'

单独运行 circos -conf ./circos.conf 这个命令报错

You are missing one or more Perl modules, require newer versions, or some modules failed to load. Use CPAN to install it as described in this tutorial

http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules

missing Clone error Can't load '/home/myan/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Clone/Clone.so' for module Clone: /home/myan/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Clone/Clone.so: undefined symbol: Perl_newSVsv_flags at /home/myan/anaconda3/envs/RepCent/lib/site_perl/5.26.2/x86_64-linux-thread-multi/XSLoader.pm line 96. at /home/myan/perl5/lib/perl5/x86_64-linux-thread-multi/Clone.pm line 16.Compilation failed in require at (eval 6) line 1. missing GD error Can't load '/home/myan/anaconda3/envs/RepCent/lib/site_perl/5.26.2/x86_64-linux-thread-multi/auto/GD/GD.so' for module GD: libwebp.so.6: cannot open shared object file: No such file or directory at /home/myan/anaconda3/envs/RepCent/bin/../lib/5.26.2/x86_64-linux-thread-multi/DynaLoader.pm line 193. at (eval 27) line 1.Compilation failed in require at (eval 27) line 1. missing GD::Polyline error Attempt to reload GD.pm aborted.Compilation failed in require at /home/myan/anaconda3/envs/RepCent/lib/site_perl/5.26.2/x86_64-linux-thread-multi/GD/Polyline.pm line 45

我把clone模块更新到0.46报错就解决了

mamba install perl-clone=0.46

运行ont数据试试

centromics -l ../ont/SRR22495385_1.fastq.gz -g ../galba.genome.annotation/fv.fna -pre ont -o ont.output -p 48

image.png

ont的数据只在7号染色体上鉴定到了一个区域

hifi数据在6号染色体上也没有鉴定到

image.png

用拟南芥的数据测试

基因组数据https://github.com/schatzlab/Col-CEN/tree/main/v1.2

ont数据

https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-10272?query=E-MTAB-10272

centromics -l ont/ERR5530736.fastq.gz -g at.col0.chr.fna -o output -p 48

less -S output/centomics.candidate_peaks.bed

image.png