SciRoKo

SciRoKo performs whole-genome microsatellite searching and resolves contig orientation to detect inverted repeats and inversion variants in genomic scaffold graphs.

Key Features:

• Contig Orientation (MAX-DIR) Resolution: Establishes the computational complexity of the contig orientation problem via a linear-time reduction from the NP-complete MAX-CUT problem.
• Greedy Heuristic Algorithm: Implements a greedy heuristic for scaffold orientation that is empirically shown to outperform other heuristics on scaffold graphs.
• Detection of Inverted Repeats and Inversion Variants: Provides a method to identify inverted repeats and inversion variants that violate single-orientation assumptions in genome assembly.
• Whole-Genome Microsatellite Search: Performs genome-wide identification and investigation of microsatellites.

Scientific Applications:

• Comparative Genomics: Facilitates comparative genomics by improving scaffold orientation and variant detection across assemblies.
• Genome Assembly Improvement: Enhances genome assembly accuracy through resolution of contig orientation and detection of inversion events.
• Structural Variation and Disease Research: Enables study of genomic structural variations, including inversions and inverted repeats, with implications for understanding genetic mechanisms in disease.

Methodology:

Applies a linear-time reduction from MAX-CUT to MAX-DIR to establish NP-completeness; implements a greedy heuristic algorithm for scaffold orientation; compares heuristic performance empirically; includes a method for identifying inverted repeats and inversion variants.