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.

本研究报道了一款新型多光学图谱支架构建工具（multi optical maps scaffolder, MOMS），其旨在利用不同酶标记的光学图谱（optical map）之间的互补信息。该流程可实现光学图谱的数据结构组织、基于路径遍历的支架构建、缺口填补与分子复用。经测试数据表明，该工具在支架构建过程中对酶的耐受性无上限。针对GM12878细胞系的基因组组装任务，MOMS显著提升了组装结果的连续性与完整性，其支架N50较初始组装最高提升144倍。本研究同时利用MOMS对马鹿、蝰蛇、穿山甲三个额外物种的基因组进行组装，并发现在染色体水平上，基于聚类的串联复制可能推动了反刍动物嗅觉受体基因家族的扩张。我们相信该工具将为高保真染色体组装、大片段结构变异检测以及染色体水平的进化分析提供助力。