Puzzle Hi-C: An accurate scaffolding software.
PLoS One
; 19(7): e0298564, 2024.
Article
em En
| MEDLINE
| ID: mdl-39008464
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.
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1
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
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Software
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Genômica
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article