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edena_overlapping_mode

By Hernandez D., Last update 1494698999
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edena_overlapping_mode description

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.