Puzzle Hi-C: an accurate scaffolding software

Lin, G.; Huang, Z.; Yue, T.; Chai, J.; Li, Y.; Yang, H.; Qin, W.; Yang, G.; Murphy, R. W.; Zhang, Y.-p.; Zhang, Z.; Zhou, W.; Luo, J.

doi:10.1101/2024.01.29.577879

bioRxiv · 10.1101/2024.01.29.577879

Puzzle Hi-C: an accurate scaffolding software

Lin, G.·Huang, Z.·Yue, T.·Chai, J.·Li, Y.·Yang, H.·Qin, W.·Yang, G.·Murphy, R. W.·Zhang, Y.-p.·Zhang, Z.·Zhou, W.·Luo, J.

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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. Current Hi-C-assisted assembling 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.

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Lin, G., Huang, Z., Yue, T., Chai, J., Li, Y., Yang, H., Qin, W., Yang, G., Murphy, R. W., Zhang, Y.-p., Zhang, Z., Zhou, W., Luo, J.. 2024-01-31. Puzzle Hi-C: an accurate scaffolding software. https://doi.org/10.1101/2024.01.29.577879

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