1. Puzzle Hi-C: An accurate scaffolding software.
- Author
-
Guoliang Lin, Zhiru Huang, Tingsong Yue, Jing Chai, Yan Li, Huimin Yang, Wanting Qin, Guobing Yang, Robert W Murphy, Ya-Ping Zhang, Zijie Zhang, Wei Zhou, and Jing Luo
- Subjects
Medicine ,Science - Abstract
High-quality, chromosome-scale genomes are essential for genomic analyses. Analyses, including 3D genomics, epigenetics, and comparative genomics rely on a high-quality genome assembly, which is often accomplished with the assistance of Hi-C data. Curation of genomes reveal that current Hi-C-assisted scaffolding algorithms either generate ordering and orientation errors or fail to assemble high-quality chromosome-level scaffolds. Here, we offer the software Puzzle Hi-C, which uses Hi-C reads to accurately assign contigs or scaffolds to chromosomes. Puzzle Hi-C uses the triangle region instead of the square region to count interactions in a Hi-C heatmap. This strategy dramatically diminishes scaffolding interference caused by long-range interactions. This software also introduces a dynamic, triangle window strategy during assembly. Initially small, the window expands with interactions to produce more effective clustering. Puzzle Hi-C outperforms available scaffolding tools.
- Published
- 2024
- Full Text
- View/download PDF