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Bioinformatics. 2011 Dec 1;27(23):3259-65. doi: 10.1093/bioinformatics/btr562. Epub 2011 Oct 13.

Fast scaffolding with small independent mixed integer programs.

Author information

1
Department of Computer Science, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland. leena.salmela@cs.helsinki.fi

Abstract

MOTIVATION:

Assembling genomes from short read data has become increasingly popular, but the problem remains computationally challenging 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 problem 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 independently. We present a technique for restricting the size of these subproblems so that they can be solved accurately with mixed integer 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 at http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/.

CONTACT:

leena.salmela@cs.helsinki.fi.

PMID:
21998153
PMCID:
PMC3223363
DOI:
10.1093/bioinformatics/btr562
[Indexed for MEDLINE]
Free PMC Article
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