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.
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.
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.