Abstract
BackgroundGenome 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.ResultsIn 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.ConclusionsOur 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.
Highlights
Genome assembly is fundamental for de novo genome analysis
Long-range scaffolding technologies can provide long-range connectivity, which can aid in resolving the complex regions
Fosmid cloning is sensitive to the quantity and quality of the input DNA, while fosmid libraries are subject to cloning bias
Summary
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. Long-range scaffolding technologies can provide long-range connectivity, which can aid in resolving the complex regions Such methods include end sequencing of fosmid clones [1], fosmid-based dilution pool sequencing [13, 14], optical mapping [15,16,17], genetic mapping with restriction site associated DNA (RAD) tags [18] and proximity ligation (Hi-C) sequencing. The data generating process for optical map construction involves mostly manual steps These steps include DNA extension and image capture, which are low throughput and inefficient. The Hi-C data provide extensive links covering large distances, the current resolution is not high enough for the local ordering of small adjacent contigs
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