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rrwick / Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
http://rrwick.github.io/Bandage/
GNU General Public License v3.0
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Functionality to extract circular sequences #60

Open sarah872 opened 6 years ago

sarah872 commented 6 years ago

Hey there, is there a command line functionality to extract circular sequences, i.e. plasmids? There is a tool called recycler github that is doing exactly this thing, but it is quite slow.

ekg commented 6 years ago

You can do this with vg, but it will also bluntify your graph. I think the specific command is in vg stats. You want to detect strongly connected components.