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SOMA
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SOMA

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.



SOMA

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.

Topic

Scaffolding

Details

  • Operation: Scaffolding; Optical map
  • Software interface: Web application; Command-line user interface
  • Language: -
  • Operating system: Linux
  • License: Not stated
    • Cost: Free
  • Version name: 2.0
  • Credit: Department of Defense Transformational Medical Technologies
  • Contact: mpop _at_ umiacs.umd.edu
  • Collection: -

Publications

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
PMID: 18356192
PMCID: PMC2373919


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