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Due to the current limitations of sequencing technologies, de novo genome assembly is typically carried out in two stages, namely contig (sequence) assembly and scaffolding. While scaffolding is computationally easier than sequence assembly, the scaffolding problem can be challenging due to the high repetitive content of eukaryotic genomes, possible mis-joins in assembled contigs and inaccuracies in the linkage information. Genome scaffolding tools either use paired-end/mate-pair/linked/Hi-C reads or genome-wide maps (optical, physical or genetic) as linkage information. Optical maps (in particular Bionano Genomics maps) have been extensively used in many recent large-scale genome assembly projects (e.g., goat, apple, barley, maize, quinoa, sea bass, among others). However, the most commonly used scaffolding tools have a serious limitation: they can only deal with one optical map at a time, forcing users to alternate or iterate over multiple maps. In this paper, we introduce a novel scaffolding algorithm called OMGS that for the first time can take advantages of multiple optical maps. OMGS solves several optimization problems to generate scaffolds with optimal contiguity and correctness. Extensive experimental results demonstrate that our tool outperforms existing methods when multiple optical maps are available, and produces comparable scaffolds using a single optical map. OMGS can be obtained from GIT.
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Accurate detection of chimeric contigs via Bionano optical maps
Abstract SummaryA chimeric contig is contig that has been incorrectly assembled, i.e. a contig that contains one or more mis-joins. The detection of chimeric contigs can be carried out either by aligning assembled contigs to genome-wide maps (e.g. genetic, physical or optical maps) or by mapping sequenced reads to the assembled contigs. Here, we introduce a software tool called Chimericognizer that takes advantage of one or more Bionano Genomics optical maps to accurately detect and correct chimeric contigs. Experimental results show that Chimericognizer is very accurate, and significantly better than the chimeric detection method offered by the Bionano Hybrid Scaffold pipeline. Chimericognizer can also detect and correct chimeric optical molecules. Availability and implementationhttps://github.com/ucrbioinfo/Chimericognizer Supplementary informationSupplementary data are available at Bioinformatics online.
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- PAR ID:
- 10393446
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Bioinformatics
- Volume:
- 35
- Issue:
- 10
- ISSN:
- 1367-4803
- Page Range / eLocation ID:
- p. 1760-1762
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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