Elmeri

Elmeri corrects optical mapping raw map data (Rmaps) by identifying overlapping Rmaps and fixing spurious and deleted cut sites to improve downstream analyses such as structural variation detection, scaffolding assembled contigs, and mis-assembly detection.

Key Features:

• Spaced seeds: Applies a novel application of spaced seeds to optical mapping data to detect informative matches between Rmaps.
• Overlap detection: Determines pairs of Rmaps that originate from the same genomic region by identifying significant overlaps.
• Error correction: Corrects errors in Rmaps specifically caused by spurious and deleted cut sites.
• Scalability: Scales to large genomes, addressing limitations of prior methods on whole-genome optical mapping datasets.
• Performance versus cOMet (speed): Processes the human genome Rmap dataset in under 15 CPU hours compared with approximately 9.9 CPU days reported for cOMet.
• Performance versus cOMet (accuracy): Improves the quality of corrected Rmaps by more than fourfold relative to cOMet.

Scientific Applications:

• Structural variation detection: Provides higher-quality Rmaps to increase the accuracy of detecting structural variants from optical mapping data.
• Scaffolding assembled contigs: Supplies corrected optical maps to support scaffolding of assembled contigs for genome assembly.
• Mis-assembly detection: Enables identification of mis-assemblies by using corrected Rmaps to validate and compare assembly structures.

Methodology:

Applies spaced seeds to optical mapping data to identify overlapping Rmap pairs from the same genomic region and correct spurious and deleted cut sites.