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SLIQ

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 forum

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SLIQ classification

SLIQ specifications

Software type:
Application/Script, Package/Module
Restrictions to use:
None
Programming languages:
Python
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes

SLIQ distribution

versioning

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SLIQ support

Maintainer

  • Rajat Roy <>

Credits

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Publications

Institution(s)

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

Link to literature

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