Maligner

Maligner aligns molecular and in silico restriction maps, including single-molecule Rmaps from optical mapping, to reference maps to support structural variant discovery and genome assembly validation.

Key Features:

• Dual Alignment Modes: Provides a dynamic programming implementation that is efficient, sensitive, and scalable to large eukaryotic genomes, and an index-based approach for rapid identification of alignments with unmatched sites present in the reference but not the query.
• Performance and Accuracy: Comparative analyses report identification of more correct alignments within comparable runtimes relative to other publicly available tools.
• M-Score Statistic: Introduces the M-Score statistic to normalize alignment scores across different restriction maps and aid selection of high-quality alignments.

Scientific Applications:

• Structural Variant Discovery: Aligns single-molecule Rmaps and in silico restriction maps to a reference to detect structural variations within genomes.
• Genome Assembly Scaffolding and Validation: Supports scaffolding of sequence assemblies and provides global validation or correction of assemblies using restriction map alignments.

Methodology:

Implemented in C++ and implements a dynamic programming alignment algorithm alongside an index-based alignment approach.