title: OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees.
abstract: The assembly of large, repeat-rich eukaryotic genomes represents a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be expensive for larger genomes. OPERA-LG is a scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, out-performing state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation and third-generation sequencing technologies. OPERA-LG provides an avenue for systematic augmentation and improvement of thousands of existing draft eukaryotic genome assemblies.
authors.affiliation: Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.|NUS Graduate School for Integrative Sciences and Engineering, Singapore, 117456, Singapore.|South Australian Health & Medical Research Institute, North Terrace, Adelaide, 5000, SA, Australia.
authors.forename: Song
authors.initials: S
authors.lastname: Gao
authors.affiliation: Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.
authors.forename: Denis
authors.initials: D
authors.lastname: Bertrand
authors.affiliation: Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.
authors.forename: Burton K H
authors.initials: BK
authors.lastname: Chia
authors.affiliation: Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore. nagarajann@gis.a-star.edu.sg.
authors.forename: Niranjan
authors.initials: N
authors.lastname: Nagarajan
mesh_terms: D000818:Animals; D020451:Contig Mapping / Q000379:methods*; D059646:Genome Size; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software