ArticleMolecular ecology2021
Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies.
Article in Molecular ecology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Characterization of a draft chromosome-scale genome assembly for the mutton snapper, Lutjanus analis.Genes & genomics · 2026Article
- A T2T Genome of the Lobed-Lip Iguazu Joana (Crenicichla tuca) Reveals Intrachromosomal Rearrangements and Trans-species Polymorphism in Cichlid Fishes.Genome biology and evolution · 2026Article
- Draft hybrid genome assembly of the photosynthetic sacoglossan Elysia crispata provides insights into sacoglossan biology.BMC genomics · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Benchmarking Hi-C scaffolders using reference genomes and de novo assemblies.Genome biology · 2026Article
- Unraveling the Genome of Epidendrum Fulgens: Demographic History and Gene Family Dynamics in a Resilient Neotropical Orchid.Genome biology and evolution · 2026Article
- Beyond inversions and deletions: the evolutionary and functional insights from translocations, fissions, and fusions in animal genomes.Heredity · 2026Review
- From Permits to Samples: Addressing Key Challenges for High-Quality Reference Genome Generation in Europe.Molecular ecology resources · 2026Review
- Molecular Responses to Temperature Changes Across Timescales in the Madagascar Ground Gecko (Paroedura picta).Molecular ecology · 2026Article
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- Genomic and translational insights into eIF2B-mediated salt tolerance in sea rice HD961.BMC biology · 2025Article
- Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae).BMC biology · 2025Article
- Ocean Genomes: reference genome resources for marine vertebrates.npj biodiversity · 2025Review
- A phased chromosome-level genome of the annelid tubeworm Galeolaria caespitosa.The Journal of heredity · 2025Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- Chromosome-level genome assembly of the spangled emperor, Lethrinus nebulosus (Forsskål 1775).Scientific data · 2025Article
- Read Mapping for Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing.BMC genomics · 2024Article
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6 authors.
Funding
Abstract
The recent development of ecological studies has been fueled by the introduction of massive information based on chromosome-scale genome sequences, even for species for which genetic linkage is not accessible. This was enabled mainly by the application of Hi-C, a method for genome-wide chromosome conformation capture that was originally developed for investigating the long-range interaction of chromatins. Performing genomic scaffolding using Hi-C data is highly resource-demanding and employs elaborate laboratory steps for sample preparation. It starts with building a primary genome sequence assembly as an input, which is followed by computation for genome scaffolding using Hi-C data, requiring careful validation. This article presents technical considerations for obtaining optimal Hi-C scaffolding results and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among the metrics that are frequently used for evaluating scaffolding results, we investigate the validity of the completeness assessment of chromosome-scale genome assemblies using single-copy reference orthologues.
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