Some details to make good vitalization for the overlapping data within Celera Assembler

gistfile1.txt

(1) If we use Celera Assembler's bogart unitiger, it will generate a file called "bests.edges" in the "4-unitigger" as one of its output directories.

(2) I wrote a simple script converting the edge list to a GML. The script can be downloaded https://github.com/PacificBiosciences/HBAR-DTK/blob/master/src/CA_best_edge_to_GML.py  

(3) Load the graph into gephi (https://gephi.org/)

(4) I typically use the following steps of different layout algorithms in Gephi to get a good layout, 

1) "YifanHu's Multilevel" to get a rough layout, the output usually catches good large scale structure and detangle the graph reasonably one so I can start to see features of the assembly overlap graph (or the string graph.)

2) "ForceAtlas 2" to smooth the path in the graph.  It is a physics based layout algorithm. If you tune the "Gravity" and "Repulsion" parameters right, one can the space-filling-curve-like layout that I showed you yesterday.

3) The "ForceAtlas 2" layout algorithm has a tendency to collapse the bubbles. I need to use the "Yifan Hu Proportional" to "open them up".

A lot of this requires some try-and-errors.  Some of the knowledge from my physics education and rough understanding of the layout algorithm helps.