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Puzzle Hi-C: An accurate scaffolding software.
- Source :
- PLoS ONE; 7/15/2024, Vol. 19 Issue 7, p1-14, 14p
- Publication Year :
- 2024
-
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. [ABSTRACT FROM AUTHOR]
- Subjects :
- COMPARATIVE genomics
GENOMICS
PUZZLES
CHROMOSOMES
COMPUTER software
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 19
- Issue :
- 7
- Database :
- Complementary Index
- Journal :
- PLoS ONE
- Publication Type :
- Academic Journal
- Accession number :
- 178439651
- Full Text :
- https://doi.org/10.1371/journal.pone.0298564