I am analysing SNPs and INDELs in several prokaryotic genomes of the same strain. My goal is to compare them with a reference genome . I would like to learn how to plot the SNPs in a circular plot. It means, that in one plot I can have my reference strain (in the inside for example) and then the other genomes could be in circules around it, showing the SNPs.
Circos is a free software for circle plots. On the website you will find a lot of examples and tutorial. Also for the installation.
Also you can choose between different plot types.
I would suggest the same, download circos and the tutorial package. I also download the tuturial package to my desktop and browse through the tutorials 6 and see circos images in folder 2-4 which shows the karyotype along with tracks. Then edits these tracks with your indels and snps. You can add more than one genomes. Do the same trick look into the tutorial folders and find the plot that very similar to what you are trying to achieve and then replace the data and start custimizing the bands, ideogram and ticks. However I think you want to plot the SNP density and the INDEL density as well (structural variation such as deletion is also useful to include). You will need to modify your your data to match circos input data i.e chr1 genomic location 11191 11192 and another value which am not sure what i am suppose to do into hs1 11191 11192 0.012 value. If you find out what is the value you need to include and how to obtain it please let me know. Also if you struggle to draw a genome without tracks let me know.
