OSLay: Optimal syntenic layout of unfinished assemblies

Daniel C. Richter; Stephan C. Schuster; Daniel H. Huson

doi:10.1093/bioinformatics/btm153

OSLay: Optimal syntenic layout of unfinished assemblies

Daniel C. Richter^*, Stephan C. Schuster, Daniel H. Huson

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

72 Citations (Scopus)

Abstract

Summary: The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure. Motivation: To enhance efficiency in the gap closure phase of a genome project it is crucial to know which contigs are adjacent in the target genome. Related genome sequences can be used to layout contigs in an assembly.

Original language	English
Pages (from-to)	1573-1579
Number of pages	7
Journal	Bioinformatics
Volume	23
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/btm153
Publication status	Published - Jul 1 2007
Externally published	Yes

ASJC Scopus Subject Areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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OSLay: Optimal syntenic layout of unfinished assemblies

Abstract

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