MOMS: A Pipeline for Scaffolding Using Multi Optical Maps

Here we reported a new multi optical maps scaffolder (MOMS) aiming at utilizing complementary information among optical maps labelled by distinct enzymes. This pipeline was designed for data structure organization, scaffolding by path traversal, gap-filling and molecule reuse of optical maps. Our tested data showed that this pipeline has uncapped enzyme tolerance in scaffolding. For the genome assembly of GM12878 cell line, MOMS significantly improved the contiguity and completeness with an up to144-fold increasing of scaffold N50 compared to initial assemblies. We also adopted MOMS to assemble three additional genomes (red deer, viper and pangolin) and found that cluster-based tandem replication may contribute to the expansion of olfactory receptors in ruminants at a chromosome level. We believe this pipeline will contribute to the high-fidelity chromosome assembly, large fragment structural variation detection and chromosome-level evolutionary analysis.