Paper Info
Title
Ldscaff: Ld-Based Scaffolding Of De Novo Genome Assemblies
Abstract
Background Genome assembly is fundamental for de novo genome analysis. 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. Results In this paper, we propose LDscaff 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 KB. 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 LDscaff treatment, the resulting Panda assembly has scaffold N50 of 3.6 MB, 2.5 times larger than the original N50 (1.3 MB). The re-assembled donkey assembly has an improved N50 length of 32.1 MB from 23.8 MB. Conclusions 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.
Year
DOI
Venue
2020
10.1186/s12859-020-03895-7
BMC BIOINFORMATICS
Keywords
DocType
Volume
De novo assembly, Maximum weighted matching, Linkage disequilibrium
Journal
21
Issue
ISSN
Citations 
21
1471-2105
0
PageRank 
References 
Authors
0.34
0
6
Name
Order
Citations
PageRank
Zicheng Zhao111.42
Yingxiao Zhou200.34
Shuai Wang341.79
Xiuqing Zhang481.83
Changfa Wang500.68
Shuai Cheng Li618430.25