ArticleGigaScience2020
Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Enhancing public health surveillance: a comparative study of platform-specific and hybrid assembly approaches in SARS-CoV-2 genome sequencing.Microbial genomics · 2025Article
- The draft genome assembly of the cosmopolitan pelagic fish dolphinfish Coryphaena hippurus.G3 (Bethesda, Md.) · 2025Article
- Genome sequencing, comparative analysis, and gene expression responses of cytochrome P450 genes inEcology and evolution · 2024Article
- Whole genome assembly and annotation of the King Angelfish (GigaByte (Hong Kong, China) · 2024Article
- Complete mitochondrial genome of the Starhead TopminnowMitochondrial DNA. Part B, Resources · 2024Article
- Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater.International journal of molecular sciences · 2023Article
- Whole-Genome Sequencing of Six Neglected Arboviruses Circulating in Africa Using Sequence-Independent Single Primer Amplification (SISPA) and MinION Nanopore Technologies.Pathogens (Basel, Switzerland) · 2022Article
- Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish, Atherinomorus stipes.Genome biology and evolution · 2022Article
- Assembly and Comparison ofMicroorganisms · 2022Article
- Benchmarking of next and third generation sequencing technologies and their associated algorithms forMolecular medicine reports · 2021Article
- Using asexual vertebrates to study genome evolution and animal physiology: Banded (Evolutionary applications · 2020Article
- Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish.GigaScience · 2020Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhole-genome sequencing data from wild-caught individuals of closely related North American killifish species (Fundulus xenicus, Fundulus catenatus, Fundulus nottii, and Fundulus olivaceus) were obtained using long-read Oxford Nanopore Technology (ONT) PromethION and short-read Illumina platforms.
findingsDraft de novo reference genome assemblies were generated using a combination of long and short sequencing reads. For each species, the PromethION platform was used to generate 30-45× sequence coverage, and the Illumina platform was used to generate 50-160× sequence coverage. Illumina-only assemblies were fragmented with high numbers of contigs, while ONT-only assemblies were error prone with low BUSCO scores. The highest N50 values, ranging from 0.4 to 2.7 Mb, were from assemblies generated using a combination of short- and long-read data. BUSCO scores were consistently >90% complete using the Eukaryota database.
conclusionsHigh-quality genomes can be obtained from a combination of using short-read Illumina data to polish assemblies generated with long-read ONT data. Draft assemblies and raw sequencing data are available for public use. We encourage use and reuse of these data for assembly benchmarking and other analyses.
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