Entering edit mode
3 months ago
marongiu.luigi
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710
I would like to compare the whole genome of different bacteria to have a quick view of features such as large deletions, recombinations, etc. In essence, what I am looking for is to create a genome atlas
or a blast atlas
even in lienar form.
What tools are available for this job, preferably running on Linux/Ubuntu machines?
Thank you
Circos is usual one: http://circos.ca/
if there is a specific workflow using circos to generate the figures OP requested i'd be interested. i know circos does a lot but seems like a tutorial/guide that gives something like BRIG would be cool. note also that BRIG has 2,000+ citations, well used tool (though circos is 7,000+)
The tool OP was referring to used to be online at the DTU in Denmark, and I did work with the authors of it, but Prof Ussery moved on and it does not seem to be maintained there any more.
This is one of the publications on it: https://backend.orbit.dtu.dk/ws/portalfiles/portal/9905767/28_912_3_PB.pdf
You are right, the tools (both genome and blast atlas) are discontinued. But I could not find an alternative yet.
other circular tools may also be used, i have a list i try to keep updated with tools. BRIG is purpose built but is an aging codebase, may not be the most modern https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Circular
BRIG and Circos seem to do the job. I'll try them, thank you.