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Updated: Jul 15, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
OSLay: optimal syntenic layout of unfinished assemblies
Daniel C Richter1, Stephan C Schuster, Daniel H Huson
1Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, 72076 Tübingen, Germany. drichter@informatik.uni-tuebingen.de
Unlabelled:
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.
Availability:
OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay.
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