ArticleGigaScience2019
Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- De novo diploid genome assembly using long noisy reads.Nature communications · 2024Article
- A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants.Science advances · 2023Article
- Advances in sequencing technologies for amyotrophic lateral sclerosis research.Molecular neurodegeneration · 2023Review
- From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research.Life (Basel, Switzerland) · 2022Review
- Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders.Scientific reports · 2022Article
- Ongoing endeavors to detect mobilization of transposable elements.BMB reports · 2022Review
- KOREF_S1: phased, parental trio-binned Korean reference genome using long reads and Hi-C sequencing methods.GigaScience · 2022Article
- A Chromosome-Level Genome Assembly of the Pygmy Mole Cricket Xya riparia.Genome biology and evolution · 2022Article
- LazyB: fast and cheap genome assembly.Algorithms for molecular biology : AMB · 2021Article
- Application of long-read sequencing to the detection of structural variants in human cancer genomes.Computational and structural biotechnology journal · 2021Review
- De novo genome assembly of a Han Chinese male and genome-wide detection of structural variants using Oxford Nanopore sequencing.Molecular genetics and genomics : MGG · 2020Article
- Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish.GigaScience · 2020Article
- Article
- Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing.Journal of clinical microbiology · 2019Review
- Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information.GigaScience · 2019Article
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10 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundLong DNA reads produced by single-molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short-read DNA fragments. For de novo assembly, Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) are the favorite options. However, PacBio's SMRT sequencing is expensive for a full human genome assembly and costs more than $40,000 US for 30× coverage as of 2019. ONT PromethION sequencing, on the other hand, is 1/12 the price of PacBio for the same coverage. This study aimed to compare the cost-effectiveness of ONT PromethION and PacBio's SMRT sequencing in relation to the quality.
findingsWe performed whole-genome de novo assemblies and comparison to construct an improved version of KOREF, the Korean reference genome, using sequencing data produced by PromethION and PacBio. With PromethION, an assembly using sequenced reads with 64× coverage (193 Gb, 3 flowcell sequencing) resulted in 3,725 contigs with N50s of 16.7 Mb and a total genome length of 2.8 Gb. It was comparable to a KOREF assembly constructed using PacBio at 62× coverage (188 Gb, 2,695 contigs, and N50s of 17.9 Mb). When we applied Hi-C-derived long-range mapping data, an even higher quality assembly for the 64× coverage was achieved, resulting in 3,179 scaffolds with an N50 of 56.4 Mb.
conclusionThe pore-based PromethION approach provided a high-quality chromosome-scale human genome assembly at a low cost with long maximum contig and scaffold lengths and was more cost-effective than PacBio at comparable quality measurements.
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