YaHS: yet another Hi-C scaffolding tool

2022/12/16 by Chenxi Zhou, Shane McCarthy, Richard Durbin · 65 citations
Biochemistry, Genetics and Molecular Biology · #Genomics and Chromatin Dynamics #Genomics and Phylogenetic Studies #RNA Research and Splicing

paper · pdf · doi:10.1093/bioinformatics/btac808

openalex publication_date 2022/12/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

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.

Citations

• De novo assembly of the <i>Aedes aegypti</i> genome using Hi-C yields chromosome-length scaffolds
• Opportunities and challenges in long-read sequencing data analysis
• Towards complete and error-free genome assemblies of all vertebrate species
• The complete sequence of a human genome

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