SOMA is a tool for scaffolding short-read based contigs of bacteria genome using optical maps. The method implemented is robust to sequencing and assembly errors. The program is available as a web-application and an open-source package.
Nagarajan N, Read TD, Pop M "Scaffolding and validation of bacterial genome assemblies using optical restriction maps." Bioinformatics. 2008 May 15;24(10):1229-35. Epub 2008 Mar 20. https://doi.org/10.1093/bioinformatics/btn102
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