Back to Search
Start Over
OMGS: Optical Map-Based Genome Scaffolding
- Source :
- Journal of computational biology : a journal of computational molecular cell biology, vol 27, iss 4, RECOMB
- Publication Year :
- 2020
- Publisher :
- eScholarship, University of California, 2020.
-
Abstract
- Due to the current limitations of sequencing technologies,de novogenome 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 fromhttps://github.com/ucrbioinfo/OMGS
- Subjects :
- Optimization problem
Theoretical computer science
Correctness
Optical Map
Computer science
Bioinformatics
Contiguity
scaffolding
Sequence assembly
Genomics
Linkage (mechanical)
Genome
Mathematical Sciences
law.invention
03 medical and health sciences
Contig Mapping
law
Information and Computing Sciences
Genetics
optical maps
Molecular Biology
Genome scaffolding
030304 developmental biology
Sequence
0303 health sciences
Contig
030302 biochemistry & molecular biology
Human Genome
food and beverages
Chromosome Mapping
Eukaryota
Sequence Analysis, DNA
DNA
Biological Sciences
de novo genome assembly
Computational Mathematics
Computational Theory and Mathematics
Modeling and Simulation
Combinatorial optimization
combinatorial optimization
Generic health relevance
Sequence Analysis
Algorithms
Software
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Journal of computational biology : a journal of computational molecular cell biology, vol 27, iss 4, RECOMB
- Accession number :
- edsair.doi.dedup.....619c00d2bf3ac3d747cc668343f6cda8