Edena (assembly mode) is a subprogram of Edena and it takes output from overlapping mode (*.ovl* file) plus assembly parameters. A set of contigs in FASTA format is outputted. The purpose of having a two step process is that the .ovl file is computed only once and can then be used to produce assemblies with different parameters.
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.