OSLay - Optimal Syntenic Layout of Unfinished Assemblies
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.
Use of the program is free for academic purposes. The software requires Java 1.5.
There is an online help providing a lof of useful information about installing and using OSLay.
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 http://bioinformatics.oxfordjournals.org/cgi/content/full/23/13/1573
If you have any comments or questions feel free to write us an email.
32 target contigs on the x-axis are sorted and oriented obtaining only one supercontig.
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/or misassemblies are apparent. OSLay's sorting reveals two putative, large inversions.