LDscaff : LD-based scaffolding of de novo genome assemblies
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Author(s)
Related Research Unit(s)
Detail(s)
| Original language | English |
|---|---|
| Article number | 570 |
| Journal / Publication | BMC Bioinformatics |
| Volume | 21 |
| Issue number | Suppl 21 |
| Online published | 28 Dec 2020 |
| Publication status | Published - 2020 |
Link(s)
| DOI | DOI |
|---|---|
| Attachment(s) | Documents
Publisher's Copyright Statement
|
| Link to Scopus | https://www.scopus.com/record/display.uri?eid=2-s2.0-85098132178&origin=recordpage |
| Permanent Link | https://scholars.cityu.edu.hk/en/publications/publication(c066037a-c04a-434a-817d-2ef8991fa1a5).html |
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.
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.
Research Area(s)
- De novo assembly, Linkage disequilibrium, Maximum weighted matching
Citation Format(s)
LDscaff: LD-based scaffolding of de novo genome assemblies. / Zhao, Zicheng; Zhou, Yingxiao; Wang, Shuai et al.
In: BMC Bioinformatics, Vol. 21, No. Suppl 21, 570, 2020.
In: BMC Bioinformatics, Vol. 21, No. Suppl 21, 570, 2020.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Download Statistics
No data available
