Fast scaffolding with small independent mixed integer programs

Motivation: Assembling genomes from short read data has become increasingly popular but the problem remains computationally chal-lenging especially for larger genomes. We study the scaffolding phase of sequence assembly where preassembled contigs are ordered based on mate pair data. Results: We present MIP Scaffolder that divides the scaffolding pro-blem into smaller subproblems and solves these with mixed integer programming. The scaffolding problem can be represented as a graph and the biconnected components of this graph can be solved inde-pendently. We present a technique for restricting the size of these subproblems so that they can be solved accurately with mixed inte-ger programming. We compare MIP Scaffolder to two state of the art methods, SOPRA and SSPACE. MIP Scaffolder is fast and produces better or as good scaffolds as its competitors on large genomes. Availability: The source code of MIP Scaffolder is freely available a