NCBI-Hackathons / NovoGraph

NovoGraph: building whole genome graphs from long-read-based de novo assemblies
MIT License
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Create optimal window "size" algorithm #2

Closed evanbiederstedt closed 6 years ago

evanbiederstedt commented 7 years ago

At the moment, we have the following ideas with regards to window size:

---try several options (e.g. -/+500 b, -/+200 b, -/+800 b) and then evaluate how these perform with metric by majority

The optimal solution would be to have varying window sizes, boundaries at locations with greatest coverage. How can we implement this? Any better algorithms come to mind? At the moment, this is a linear search algorithm, and would be the bottleneck for this code.