question on graph compaction

COMBINE-lab / cuttlefish

Building the compacted de Bruijn graph efficiently from references or reads.

BSD 3-Clause "New" or "Revised" License

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question on graph compaction #5

Open kevyin opened 3 years ago

kevyin commented 3 years ago

Hi thank you for cuttlefish,

I have an output from cuttlefish at k=31

The unitigs don't seem to be maximal, there are multiple unitigs in a row shouldn't they be joined merged?

cuttlefish_k31

I hope I didnt do something wrong Thanks in advance

jamshed commented 3 years ago

Hi @kevyin, thank you for using cuttlefish! We'll need some more information to look into this. Would it be possible for you to provide the reference data that you had used in this experiment, or any small enough sample where you're observing such a scenario? Besides, please provide the commands that you used here. Also, what tool have you used for the visualization?