Orienting Ordered Scaffolds: Complexity and Algorithms

Despite the recent progress in genome sequencing and assembly, many of currently available assembled genomes come a draft form. Such consist large number genomic fragments (scaffolds), whose order and/or orientation (i.e., strand) are unknown. There exist various scaffold assembly methods, which attempt to determine scaffolds along chromosomes. Some these methods (e.g., based on FISH physical mapping, chromatin conformation capture, etc.) can infer scaffolds, but not necessarily their orientation. This leads special case problem deducing each scaffold) with known scaffolds. We address orientating ordered as an optimization given weighted orientations pairs coming from pair-end reads, long or homologous relations). formalize this using notion graph graph, where vertices correspond contigs edges represent connections between them). prove that is NP-hard, present polynomial-time algorithm for solving its case, imposed relatively at most two other further develop FPT general OOS problem.