The Ploidulator (I'll be back...)

Sep 5, 2014 at 5:47 AM
Some time ago Amber posted about a tool for ddradseq which she christened The Ploidulator (see [discussion:471645] for details). We now have 4 people working on extending this as part of a series of student projects. The idea is that we will now integrate the full pipeline. This involves;
  • getting reads
  • producing a similarity or relatedness matrix
  • clustering (via MCL)
  • visualisation of the clusters
  • Ploidy detection (integrating Phase)
Thoughts and suggestions - especially in relation to read data, sparse matrices, MCL implementations et al - most welcome. This is a short intro post, with more comments to come.