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Linkage mapping provides a practical way to anchor de novo genome assemblies into chromosomes and to detect chimeric or otherwise erroneous contigs. Such anchoring improves with higher number of markers and individuals, as long as the mapping software can handle all the information. Recent software Lep-MAP3 can robustly construct linkage maps for millions of genotyped markers and on thousands of individuals, providing optimal maps for genome anchoring. For such large datasets, automated and robust genome anchoring tool is especially valuable and can significantly reduce intensive computational and manual work involved.

Lep-Anchor: automated construction of linkage map anchored haploid genomes