MUM

MUM detects structural variants in genomic assemblies by analyzing whole-genome alignments to identify insertions, deletions, tandem duplications, inversions, and translocations greater than 50 base pairs for assembly-based SV discovery and comparative genomics.

Key Features:

• Alignment engine: Operates on whole-genome alignments produced by MUMmer's nucmer.
• SV types detected: Identifies insertions, deletions, tandem duplications, inversions, and translocations.
• Size threshold: Calls structural variants larger than 50 base pairs.
• Input data: Designed to work on contiguous de-novo assemblies derived from third-generation sequencing technologies.
• Implementation: Packaged as a single bash script for automated processing of alignments.
• Benchmarking and performance: Validated against five other whole-genome-alignment SV callers on simulated yeast, plant, and human datasets with superior performance on simulated data and comparable results on two real human genome datasets.

Scientific Applications:

• Assembly-based SV discovery: Detection of structural variants directly from de-novo genome assemblies.
• Inversion identification: Accurate calling of inversions as part of the SV spectrum.
• Comparative genomics: Analysis of structural variation across species including yeast, plants, and humans.
• Method benchmarking: Evaluation and comparison of SV-calling performance using simulated and real genome datasets.

Methodology:

MUM analyzes whole-genome alignments generated by MUMmer's nucmer and parses those alignments to call insertions, deletions, tandem duplications, inversions, and translocations larger than 50 bp.