OSLay 1.0

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.<br /><br />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.<br /><br />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.<br /><br />Feature list:<br /><br /> * reads two fasta files (contigs of target assembly and reference sequence/assembly) and one BLAST/NUCmer file<br /> * is able to sort and order both axes simultaneously if target and reference sequences are unfinished assemblies<br /> * is applicable to either procaryotic and eukaryotic genomes<br /> * has several possibilities to filter and adapt data such as trimming of unmatched contig ends, filtering blast hits,...<br /> * exports result views to several graphical formats (.jpg, .gif, .eps, .png and .svg.)<br /> * modifies or generates a new ACE file directly importable into Consed for simplified primer design<br /> * provides useful zooming functionality<br /> * facilitates visual analysis of assemblies and meta-assemblies e.g. occurences of recombinations or misassemblies respectively.

Requirements:	No special requirements
Platforms:	Mac, Mac OSX
Keyword:	Adapt,  Applicable,  Assemblies,  Blast,  Blastnucmer,  Contig,  Eukaryotic,  Exports,  Filter,  Filtering,  Genomes,  Order,  Possibilities,  Procaryotic,  Simultaneously,  Trimming,  Unfinished,  Unmatched
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