YaHS: yet another Hi-C scaffolding tool
Open accessPublished version of a preprint
Abstract
Summary: We present YaHS, a user-friendly command-line tool for the construction of chromosome-scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal input from users (an assembly file and an alignment file) which is compatible with similar tools and provides assembly results in multiple formats, thereby enabling rapid, robust and scalable construction of high-quality genome assemblies with high accuracy and contiguity. Availability and implementation: YaHS is implemented in C and licensed under the MIT License. The source code, documentation and tutorial are available at https://github.com/sanger-tol/yahs. Supplementary information: Supplementary data are available at Bioinformatics online.
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Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to long-read sequencing technologies, DNA proximity ligation sequencing techniques, and genome sequencing consortia.
“Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to the development of long-read sequencing technologies like the Pacific Biosciences and Oxford Nanopore platforms (52); the development of DNA proximity ligation sequencing techniques, like Hi-C, for genome scaffolding (53–55); and the efforts of genome sequencing consortia (1, 2, 4, 56)”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [53]
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Opportunities and challenges in long-read sequencing data analysis
Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530 · see citing works
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Topological Approaches in Animal Comparative Genomics
Schultz, D. T., & Simakov, O. (2026) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-030424-084541 · Cited by 1 · see citing works
- Authors
- Zhou, C., McCarthy, S. A., & Durbin, R.
- Affiliations
- University of Cambridge (GB)
- Corresponding author
- Durbin, Richard
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-12-16
- Volume
- 39
- Issue
- 1
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC9848053
- OpenAlex
- W4311663808
- Cited by
- 2,440
- References
- 1
- Citations by year
- 2026: 743 · 2025: 751 · 2024: 626 · 2023: 302 · 2022: 18
- FWCI
- 138.39
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Wellcome (207492, 218328, 220540)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- Hi-C scaffolding, genome assembly, long-read alignment, contiguity
- MeSH terms
- Documentation, Software
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