HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes

HAlign-G is a fast and memory-efficient tool for large-scale multiple genome alignment. Using BWT-FM-LIS with an optimized K-band algorithm and star alignment strategy, it supports intra-species (HAlign-G1) and cross-species (HAlign-G2) alignment. Benchmarks show superior accuracy, efficiency, and memory use compared with existing methods. HAlign-G1 excels in speed and quality for intra-species data for multiple sequence alignment, while HAlign-G2 offers higher accuracy and structural variant detection for multiple genome alignment. Both versions handle millions of SARS-CoV-2 genomes and thousands of human chromosomes, enabling reliable evolutionary studies and supporting the construction of more stable phylogenetic trees, while enhancing Progressive Cactus performance.

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Publication Details

Journal
Genome biology
Published
2025-11-28
DOI
https://doi.org/10.1186/s13059-025-03881-3
Citations
3
Primary Topic
Genomics and Phylogenetic Studies
Type
article
Field-Weighted Citation Impact
2.42

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article

HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes

Qinzhong Tian, Quan Zou, Yixiao Zhai, Pinglu Zhang et al.
3 citations
Genome biology
Genomics and Phylogenetic Studies
2.42
article

HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes

Qinzhong Tian, Quan Zou, Yixiao Zhai, Pinglu Zhang, Furong Tang, Yizheng Wang, Tong Zhou, Ximei Luo, Yanming Wei
article en
3 citations

Abstract

HAlign-G is a fast and memory-efficient tool for large-scale multiple genome alignment. Using BWT-FM-LIS with an optimized K-band algorithm and star alignment strategy, it supports intra-species (HAlign-G1) and cross-species (HAlign-G2) alignment. Benchmarks show superior accuracy, efficiency, and memory use compared with existing methods. HAlign-G1 excels in speed and quality for intra-species data for multiple sequence alignment, while HAlign-G2 offers higher accuracy and structural variant detection for multiple genome alignment. Both versions handle millions of SARS-CoV-2 genomes and thousands of human chromosomes, enabling reliable evolutionary studies and supporting the construction of more stable phylogenetic trees, while enhancing Progressive Cactus performance.

Genome biologyVol. 26(1)
Xidian University (CN), University of Electronic Science and Technology of China (CN), Beijing Academy of Social Sciences (CN), Quzhou City People's Hospital (CN), Quzhou University (CN), Tsinghua University (CN)
National Natural Science Foundation of China, China Postdoctoral Science Foundation, Natural Science Foundation of Zhejiang Province
Openalex Percentile: Top 10%
Genomics and Phylogenetic Studies
2.42
DOIOpen Access PDFOpenAlex
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HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes — Qinzhong Tian, Quan Zou, et al. · Genome biology (2025) | TGRS Research Map | TGRS