SCARPA: scaffolding reads with practical algorithms | Zendy

Nilgun Donmez | Zendy; Michael Brudno | Zendy

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SCARPA: scaffolding reads with practical algorithms

Author(s) -

Nilgun Donmez,

Michael Brudno

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts716

Subject(s) - scaffold , contig , computer science , algorithm , heuristic , process (computing) , genome , biology , artificial intelligence , programming language , genetics , gene

Scaffolding is the process of ordering and orienting contigs produced during genome assembly. Accurate scaffolding is essential for finishing draft assemblies, as it facilitates the costly and laborious procedures needed to fill in the gaps between contigs. Conventional formulations of the scaffolding problem are intractable, and most scaffolding programs rely on heuristic or approximate solutions, with potentially exponential running time.

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