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Background <p>Studying 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.</p> Results <p>Through 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 – <i>S. cerevisiae, L. tarentolae, A. thaliana</i>, and <i>H. sapiens</i>. 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.</p> Conclusions <p>We 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.</p>

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Benchmarking Hi-C scaffolders using reference genomes and de novo assemblies

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月10日

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  • Aakash Sur,
  • William Stafford Noble,
  • Peter J. Myler

摘要

Background

Studying 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.

Results

Through 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.

Conclusions

We 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.