Paper Info
Title
OMGS - Optical Map-Based Genome Scaffolding.
Abstract
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 article, we introduce a novel scaffolding algorithm called OMGS (Optical Map-based Genome Scaffolding) 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.
Year
DOI
Venue
2019
10.1089/cmb.2019.0310
JOURNAL OF COMPUTATIONAL BIOLOGY
Keywords
Field
DocType
combinatorial optimization,de novo genome assembly,optical maps,scaffolding
Genome,Contiguity,Biology,Correctness,Genomics,Combinatorial optimization,Theoretical computer science,Contig,Genetics,Optimization problem,Sequence assembly
Conference
Volume
Issue
ISSN
27.0
4
1066-5277
Citations 
PageRank 
References 
1
0.36
0
Authors
3
Name
Order
Citations
PageRank
Weihua Pan111.04
Tao Jiang21809155.32
Stefano Lonardi3202.80