Lep-Anchor

Lep-Anchor anchors de novo genome assemblies onto chromosomes using dense linkage maps to determine contig order and orientation for improved assembly completeness and accuracy.

Key Features:

• Automated genome anchoring: Automates anchoring of genome assemblies using dense linkage maps to infer chromosomal positions, order, and orientation of contigs.
• Large-dataset support: Processes millions of genotyped markers across thousands of individuals for large-scale linkage and anchoring analyses.
• Uncertainty management: Incorporates uncertainty in linkage map positions arising from low recombination regions, different cross types, or variable map quality into the anchoring procedure.
• Chimeric contig detection and correction: Identifies and resolves chimeric contigs to improve assembly accuracy.
• Integration of additional alignments: Refines contig order and orientation using contig-contig alignments, single read alignments, and alternative genome assemblies, reporting up to ~70% improvement in anchoring completeness without compromising accuracy.
• Performance comparison: Demonstrates greater anchoring completeness and speed than ALLMAPS while maintaining comparable accuracy, with Chromonomer noted as faster but exhibiting significant accuracy limitations.

Scientific Applications:

• De novo genome assembly anchoring: Assigns and orients contigs to chromosomes for newly assembled genomes to produce chromosome-scale assemblies.
• Linkage map construction and refinement: Uses dense linkage data to resolve marker positions and improve map-informed ordering of assembly contigs.
• Genetic and comparative studies: Produces more complete and accurately oriented assemblies to support downstream analyses such as mapping, QTL analysis, and comparative genomics.

Methodology:

Integrates dense linkage maps with contig-contig alignments, single read alignments, and alternative genome assemblies; models and incorporates linkage map positional uncertainty; detects and corrects chimeric contigs; and applies alignment-based strategies to optimize contig order and orientation.