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HingeAssembler / HINGE

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"
http://genome.cshlp.org/content/27/5/747.full.pdf+html?sid=39918b0d-7a7d-4a12-b720-9238834902fd
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Question: Which graph did you print for the biorxiv preprint #63

Closed ghost closed 8 years ago

ghost commented 8 years ago

When I run Hinge I get different graph files. What is the meaning of the different graphs?

Which one did you print with Gephi for the publication / which one do you suggest?

ilanshom commented 8 years ago

The .G2s.graphml shows the two strands separately, while .G2c.graphml (which is the one we used for the biorxiv preprint) has the two strands combined. The other graphs are before the pruning and clipping operations.

When you open it in Gephi you will need to use ForceAtlas2 to generate a nice layout. Alternatively, you can see what we did to generate the figures on an ipython notebook that is available here. In the notebook we also explain how we color the graphs on the preprint according to the contigs produced by hgap.

ghost commented 8 years ago

Thanks a lot