CODEWITHSUNDEEP
bioinformaticsphylogenyggtreecircosape-phylo
Vinit24
Vinit24

Reputation: 1

How to create a circos plot

I've 50 COVID samples (PE fastq reads) along with clades and lineage data for each sample. I am doing a phylogenetic analysis.My workflow to produce the tree is as following: raw reads (.fastq) --> assembly (SPades) --> RagTag (scaffolding) --> mafft (MSA) --> IQtree (phylogenetic tree) I need to visualize the obtained phylogenetic tree in a circular circos plot using bash, python or R script as a output in pdf/image. How to do this? Is there any scripts available to produce such output? or is there any way to obtained the output by just providing input- tree file and sample-clade-lineage info as data. Please guide me with this. The image provided is an example of output I want. example image example image

I have used Nextclade-CLI but it does not generate the output what I wanted to have. I tried Itol but it is web based. I also used ggtree and ete3 but was not able to produce such output. I need something that can easily provide output by inputting tree file and metadata.

Upvotes: 0

Views: 214

Answers (1)

Adolf Tulenkov
Adolf Tulenkov

Reputation: 1

I think you are better off using iTOL and then drawing whatever you want on it with a vector graphic redactor like Inkscape. If you do not like web-based soft, you can try other phylogeny tree redactors like FigTree. This is probably possible to draw some part of your graph in CIRCOS, however this program require some understanding from user to make it work and I do not use it so in depth. So I advise you to check the CIRCOS course and tutorials for some info, in addition you can ask your question in the Google group

Upvotes: 0

Related Questions