Does anyone know what tools are used to construct this beautiful genome map? The research paper didn't mention how to construct this map. Link to paper: https://www.sciencedirect.com/science/article/pii/S2052297515000773?via%3Dihub
Circos: http://circos.ca/ (or a copy of it written for another language, depending on what the paper's authors used — probably best to check with them).
$\begingroup$ hey thanks! any tutorial on how to make those maps in circos? i found out that circos kinda hard to use for beginners $\endgroup$ Nov 15, 2021 at 9:32
1$\begingroup$ To expand on this, Circos is an older Perl executable script, a mighty complex one with loads of functionality, but awkward input that requires a few trials. For scripting in Python/Julia/JS the Plotly module has a tool, albeit it slightly trickier to overlay stuff one than for a scatter, while in R there are a few options. the RCircos is the R package that is more faithful to the original Perl functionality I believe. $\endgroup$ Nov 15, 2021 at 9:34
1$\begingroup$ The quick start guides are the best way to get going with the original Circos: circos.ca/documentation/tutorials/quick_guide It looks complicated, but it is no more difficult to use than any of its imitations, which all require as much work in the end, as the same data are required to make the desired figure. $\endgroup$ Nov 15, 2021 at 17:35
I tried to used Circos for my MSc Thesis but didn't have enough time to actually learn how to use so I managed to find a less fancy but also cool version of it called ClicO.FS which is an interactive web-based service of Circos (as the title of the article below says).
Possibly BRIG (blast ring image generator) was used
I also catalog other tools here if interested https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG
1$\begingroup$ Circos appears to have been published at least two years before BRIG, but no citation. Unfortunate. $\endgroup$ Nov 17, 2021 at 4:37