Edena (overlapping mode) is a subprogram of Edena assembler and it computes the transitively reduced overlaps graph from reads files. This structure is then stored together with the sequence reads in a binary file suffixed with “.ovl”.
Parent program: edena
Edena is an overlaps-graph-based de novo assembler. The key steps of Edena are: first, the short reads data set is processed to remove redundant information; second, all overlaps of a minimum size are computed, and an overlap graph is constructed; third, the graph is cleaned by removing transitive and spurious edges and by resolving bubbles. Finally, all contigs of a minimum size that are unambiguously represented in the graph are provided as an output.