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Predicts relative positions and orientations of the contigs, yielding a directed contig graph. SLIQ provides a set of simple linear inequalities derived from the geometry of contigs on the line. It produces a reduced subset of reliable mate pairs and thus a sparser graph which results in a simpler optimization problem for the scaffolding algorithm. The output of this scaffolder can either be used as draft scaffolds or as a reasonable starting point for refinement with more complex optimization procedures used in other scaffolders.

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SLIQ classification

SLIQ specifications

Software type:
Application/Script, Package/Module
Restrictions to use:
Programming languages:
Command line interface
Operating system:
Computer skills:

SLIQ distribution


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SLIQ support


  • Rajat Roy <>


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Department of Computer Science, Rutgers, The State University of New Jersey, Piscataway, NJ, USA

Link to literature

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