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OSLay - Optimal Syntenic Layout of Unfinished Assemblies

OSLay logo

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 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.

Feature list:

  • reads two fasta files (contigs of target assembly and reference sequence/assembly) and one BLAST/NUCmer file

  • is able to sort and order both axes simultaneously if target and reference sequences are unfinished assemblies

  • is applicable to either procaryotic and eukaryotic genomes

  • has several possibilities to filter and adapt data such as trimming of unmatched contig ends, filtering blast hits,...

  • exports result views to several graphical formats (.jpg, .gif, .eps, .png and .svg.)

  • modifies or generates a new ACE file directly importable into Consed for simplified primer design

  • provides useful zooming functionality

  • facilitates visual analysis of assemblies and meta-assemblies e.g. occurences of recombinations or misassemblies respectively.


Use of the program is free for academic purposes. The software requires Java 1.5.

For a quick start with OSLay you may want to download an example project file (.cgv) of a Bacillus anthracis assembly. If you use this program for your own research please cite our software.


There is an online help providing a lof of useful information about installing and using OSLay.

Reference and Contact

D.C. Richter, S.C. Schuster, D.H. Huson. OSLay: optimal syntenic layout of unfinished assemblies, Bioinformatics. 2007 Jul 1;23(13):1573-9.

Epub 2007 Apr 26

If you have any comments or questions feel free to write us an email.


OSLay standard views

32 target contigs on the x-axis are sorted and oriented obtaining only one supercontig.


reference genome unfinished

The reference sequence on the y-axis is unfinished as well. In this case, the target contigs can be partially linked as single supercontigs.


recombinations and misassemblies apparent

Recombinations and/or misassemblies are apparent. OSLay's sorting reveals two putative, large inversions.


user options

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