ArticleGenome biology2026
Benchmarking Hi-C scaffolders using reference genomes and de novo assemblies.
Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Chromosome-Level Genome Assembly and Annotation of theJournal of fungi (Basel, Switzerland) · 2026Article
- A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes.Nucleic acids research · 2024Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads.Frontiers in bioinformatics · 2024Article
- Ten simple rules for defining a computational biology project.PLoS computational biology · 2023Article
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Authors and funding
3 authors.
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Abstract
backgroundStudying a new species using high-throughput sequencing requires a high-quality reference genome. However, assembling chromosome length sequences remains challenging. Recent advances in chromatin conformation capture (Hi-C) have provided a new approach to scaffolding genome assemblies, and the last ten years have seen a proliferation of such methods. However, to our knowledge no comprehensive benchmarking of Hi-C scaffolders has been conducted to date.
resultsThrough a literature review we identify the most popular Hi-C scaffolders - Lachesis, HiRise, 3d-dna, SALSA, and AllHiC. We test their ability to scaffold four well studied genomes - S. cerevisiae, L. tarentolae, A. thaliana, and H. sapiens. Scaffolders are tasked with both scaffolding fragmented versions of the reference genome as well as de novo assemblies derived from long read datasets. We find that all scaffolders can exceed 80% accuracy under ideal circumstances but that their performance quickly deteriorates under more challenging conditions. Surprisingly, many scaffolders also show poor performance on the best assemblies, where contigs are near chromosome length. Overall, we find that HiRise and Lachesis offer the best performance on average across all conditions.
conclusionsWe compare the performance of five Hi-C scaffolders using multiple reference species under both ideal and real-life conditions, thereby illuminating their strengths and weaknesses.
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