I've been looking at the snippets and examples in the source code but none of them mention using paired read information. Is it possible with GATB to create graphs that are decorated using paired read information?
It is not directly possible to support paired reads from the graph API of GATB-CORE.
However, we have recently added the possibility to decorate the nodes of the graph with any kind of information, so it would be possible (after graph creation) to map information from the reads (paired reads in your case) to the nodes of the de Bruijn graph.
This new feature is done by using a minimal perfect hash function library, EMPHF; such a hash function takes about 2.61 bits per node (to be added to the about 8.6 bits per node for storing the de Bruijn graph). There is of course to add N bits per node, where N is the information you want to decorate the nodes with.
If you are interested, I could add some snippets showing how to decorate the nodes with information from paired reads (assuming that two consecutive reads makes a pair)