GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C

Shun Ouchi; Rei Kajitani; Takehiko Itoh

doi:10.1186/s13059-023-03006-8

GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C

Genome Biol. 2023 Jul 11;24(1):162. doi: 10.1186/s13059-023-03006-8.

Authors

Shun Ouchi¹, Rei Kajitani¹, Takehiko Itoh²

Affiliations

¹ School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8550, Japan.
² School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8550, Japan. takehiko@bio.titech.ac.jp.

Abstract

Chromosome-level haplotype-resolved genome assembly is an important resource in molecular biology. However, current de novo haplotype assemblers require parental data or reference genomes and often fail to provide chromosome-level results. We present GreenHill, a novel scaffolding and phasing tool that considers various assemblers' contigs as input to reconstruct chromosome-level haplotypes using Hi-C without parental or reference data. Its unique functions include new error correction based on Hi-C contacts and the simultaneous use of Hi-C and long reads. Benchmarks reveal that GreenHill outperforms other approaches in contiguity and phasing accuracy, and the majority of chromosome arms are entirely phased.

Keywords: Genome assembly; Haplotype; Hi-C; Phasing; Scaffolding.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Benchmarking
Haplotypes
Tool Use Behavior*