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Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing efforts, the information provided millions of existed whole-genome sequencing data have not been fully utilized to resolve the task of scaffolding. Genetic recombination patterns in population data indicate non-random association among alleles at different loci, can provide physical distance signals to guide scaffolding.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this paper, we propose<jats:italic>LDscaff<\/jats:italic>for draft genome assembly incorporating linkage disequilibrium information in population data. We evaluated the performance of our method with both simulated data and real data. We simulated scaffolds by splitting the pig reference genome and reassembled them. Gaps between scaffolds were introduced ranging from 0 to 100\u00a0KB. The genome misassembly rate is 2.43% when there is no gap. Then we implemented our method to refine the Giant Panda genome and the donkey genome, which are purely assembled by NGS data. After<jats:italic>LDscaff<\/jats:italic>treatment, the resulting Panda assembly has scaffold N50 of 3.6\u00a0MB, 2.5 times larger than the original N50 (1.3\u00a0MB). The re-assembled donkey assembly has an improved N50 length of 32.1\u00a0MB from 23.8\u00a0MB.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our method effectively improves the assemblies with existed re-sequencing data, and is an potential alternative to the existing assemblers required for the collection of new data.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-020-03895-7","type":"journal-article","created":{"date-parts":[[2020,12,28]],"date-time":"2020-12-28T07:02:43Z","timestamp":1609138963000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["LDscaff: LD-based scaffolding of de novo genome assemblies"],"prefix":"10.1186","volume":"21","author":[{"given":"Zicheng","family":"Zhao","sequence":"first","affiliation":[]},{"given":"Yingxiao","family":"Zhou","sequence":"additional","affiliation":[]},{"given":"Shuai","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Xiuqing","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Changfa","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Shuaicheng","family":"Li","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,12,28]]},"reference":[{"issue":"4","key":"3895_CR1","doi-asserted-by":"publisher","first-page":"1513","DOI":"10.1073\/pnas.1017351108","volume":"108","author":"S Gnerre","year":"2011","unstructured":"Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, et al. 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